Godaddy says give it 48 hours.
When I updated mine it took a couple hours for me to see it. So I SSHed to Sweden (I'm in Arizona) and it did take a about 48 hours to go 'round the globe. 

The IPv4 nameserver will answer if the IPv6 nameservers go down. Thats the point of naming more than 1 nameserver. Redundancy.
Just to verify this, and you could do the same, I firewalled incoming udp traffic destined for the IPv6 address on port 53 of my nameserver.
It still answered queries on the v4 address and this was verified via logs. Take care.

AHA I got it to work.

Each whois server has its own flags that can be used. For example if you use 'whois -h whois.arin.net ...' you can use -- to seperate whois server switches from the whois command itself.
Typing whois -h www.arin.net -- -? gave me a list of switches accepted by the whois server.
So i typed this:
whois -h whois.arin.net -- + z 2001:4978:12e:a::1
Which produced:  ( and the Daily Test liked this output )

[Querying whois.arin.net]
[whois.arin.net]
#
# The following results may also be obtained via:
# http://whois.arin.net/rest/nets;q=2001:4978:12e:a::1?showDetails=true&showARIN=false
#


# start

NetRange:       2001:4978:: - 2001:4978:FFFF:FFFF:FFFF:FFFF:FFFF:FFFF
CIDR:           2001:4978::/32
OriginAS:      
NetName:        YOURORG-NB6-AR-1
NetHandle:      NET6-2001-4978-1
Parent:         NET6-2001-4800-0
NetType:        Direct Allocation
NameServer:     NS4.YOUR.ORG
NameServer:     NS1.YOUR.ORG
NameServer:     NS3.YOUR.ORG
NameServer:     NS2.YOUR.ORG
RegDate:        2005-10-20
Updated:        2005-10-20
Ref:            http://whois.arin.net/rest/net/NET6-2001-4978-1

OrgName:        YOUR.ORG, INC.
OrgId:          YOURO
Address:        840 W Lake St #406
City:           Roselle
StateProv:      IL
PostalCode:     60172
Country:        US
RegDate:        2002-12-18
Updated:        2005-10-12
Ref:            http://whois.arin.net/rest/org/YOURO

OrgTechHandle: KDA6-ARIN
OrgTechName:   Day, Kevin
OrgTechPhone:  +1-312-884-7618
OrgTechEmail:  noc@your.org
OrgTechRef:    http://whois.arin.net/rest/poc/KDA6-ARIN

RAbuseHandle: KDA6-ARIN
RAbuseName:   Day, Kevin
RAbusePhone:  +1-312-884-7618
RAbuseEmail:  noc@your.org
RAbuseRef:    http://whois.arin.net/rest/poc/KDA6-ARIN

RNOCHandle: KDA6-ARIN
RNOCName:   Day, Kevin
RNOCPhone:  +1-312-884-7618
RNOCEmail:  noc@your.org
RNOCRef:    http://whois.arin.net/rest/poc/KDA6-ARIN

RTechHandle: KDA6-ARIN
RTechName:   Day, Kevin
RTechPhone:  +1-312-884-7618
RTechEmail:  noc@your.org
RTechRef:    http://whois.arin.net/rest/poc/KDA6-ARIN

# end


# start

NetRange:       2001:4978:100:: - 2001:4978:1FF:FFFF:FFFF:FFFF:FFFF:FFFF
CIDR:           2001:4978:100::/40
OriginAS:       AS19255
NetName:        SIXXS-USCHI02-SUBNETS
NetHandle:      NET6-2001-4978-100-1
Parent:         NET6-2001-4978-1
NetType:        Reassigned
Comment:        SixXS allocation for Your.org Chicago,IL PoP - This allocation is used for /48 subnets. - For more details, query whois.sixxs.net - More information can be found at http://www.sixxs.net/ - Abuse reports should go to abuse@sixxs.net
RegDate:        2007-10-30
Updated:        2007-10-30
Ref:            http://whois.arin.net/rest/net/NET6-2001-4978-100-1

OrgName:        SixXS
OrgId:          SIXXS-1
Address:        Kelvinstraat 63
City:           Ede
StateProv:      Utrecht
PostalCode:     6716 BV
Country:        NL
RegDate:        2007-10-30
Updated:        2007-10-30
Ref:            http://whois.arin.net/rest/org/SIXXS-1

OrgTechHandle: STRA1-ARIN
OrgTechName:   SixXS Technical Role Account
OrgTechPhone:  +31 318 648688
OrgTechEmail:  info@sixxs.net
OrgTechRef:    http://whois.arin.net/rest/poc/STRA1-ARIN

# end

Also most of the time for other addresses I just seem to get this:

whois 2001:4978:12e:a::1
[Querying whois.arin.net]
[whois.arin.net]
#
# Query terms are ambiguous.  The query is assumed to be:
#     "n 2001:4978:12e:a::1"
#
# Use "?" to get help.
#

#
# The following results may also be obtained via:
# http://whois.arin.net/rest/nets;q=2001:4978:12e:a::1?showDetails=true&showARIN=false
#

YOUR.ORG, INC. YOURORG-NB6-AR-1 (NET6-2001-4978-1) 2001:4978:: - 2001:4978:FFFF:FFFF:FFFF:FFFF:FFFF:FFFF
SixXS SIXXS-USCHI02-SUBNETS (NET6-2001-4978-100-1) 2001:4978:100:: - 2001:4978:1FF:FFFF:FFFF:FFFF:FFFF:FFFF


#
# ARIN WHOIS data and services are subject to the Terms of Use
# available at: https://www.arin.net/whois_tou.html
#

Course now the test won't except the output. It keeps saying its invalid. This is what I'm pasting:

[Querying whois.arin.net]
[Redirected to rwhois.he.net:4321]
[Querying rwhois.he.net]
[rwhois.he.net]
%rwhois V-1.5:0012b7:01 ops.he.net (HE-RWHOISd v:r255,m1:r255)
network:ID:NET-2001:470:1F0F:8BB::/64
network:Auth-Area:nets
network:Class-Name:network
network:Network-Name:NET-2001:470:1F0F:8BB::/64
network:Parent;I:NET-2001:470:1F0F::/48
network:Parent;I:NET-2001:470::/32
network:IP-Network:2001:470:1f0f:8bb::/64
network:Tech-Contact;I:POC-HE-NOC
network:Abuse-Contact;I:POC-HE-ABUSE
network:NOC-Contact;I:POC-HE-NOC
network:Name-Server:ns1.boxteks.net
network:Name-Server:ns2.boxteks.net
network:Name-Server:ns3.boxteks.net
network:Created:20110104023336000
network:Updated:20110106143357000

contact:ID:POC-HE-NOC
contact:Auth-Area:contacts
contact:Class-Name:contact
contact:Name:Network Operations Center
contact:Company:Hurricane Electric
contact:Street-Address:760 Mission Ct
contact:City:Fremont
contact:Province:CA
contact:Postal-Code:94539
contact:Country-Code:US
contact:Phone:+1-510-580-4100
contact:E-Mail:noc@he.net
contact:Created:20100901200738000
contact:Updated:20100901200738000

contact:ID:POC-HE-ABUSE
contact:Auth-Area:contacts
contact:Class-Name:contact
contact:Name:Abuse Department
contact:Company:Hurricane Electric
contact:Street-Address:760 Mission Ct
contact:City:Fremont
contact:Province:CA
contact:Postal-Code:94539
contact:Country-Code:US
contact:Phone:+1-510-580-4100
contact:E-Mail:abuse@he.net
contact:Created:20100901200738000
contact:Updated:20100901200738000
contact:Comment:For email abuse (spam) only

%ok

OMG. I shut off ip6tables and it works. How n00bish.
*face_palm* 

I guess I should mention that I'm tryin to use it on CentOS 5.5
On FreeBSD I run whois -m 2001:470:1f0f:8bb::666
route6:     2001:470::/32
descr:      Hurricane Electric
            55 South Market St
            San Jose, CA
origin:     AS6939
notify:     noc-dist@he.net
mnt-by:     HE-NOC
changed:    mtindle@he.net 20081217  #20:25:45Z
source:     RADB

But on Linux I have no -m option. And every switch I try gives me nothing, hangs or errors. So I'm at a loss.

Even afte reading the man pages and looking around the internet... I can not seem to find how to properly format a whois request to query an IPv6 IP. On FreeBSD I can use the -m option but the test doesn't seem to like my output. On Linux none of the switches on the man page work for querying an IPv6 IP. How do I format the query to get the required results? Thnks in advance.