They cannot work with the current tools. We do translate properly the quota system calls used by the tools into the 64-bit kernel. However, the kernel uses a 64-bit time_t in the quota.user and quota.group records, but the quota tools cannot grok this. This also points out another problem wrt. Alpha systems, you cannot swap ext2 disks with quotas between 64-bit and 32-bit systems, although it would work if you force the quota database to be updated at the time of the disk swap so the quota files are completely rebuilt on the new system. A solution will involve some hacks to the quota tools so they understand the 64-bit kernel quota files. This is the fastest/easiest way towards a fix at this time.
Fixed in latest build via quota-1.66-6 which has my fixes for this problem.