Just FYI, I discovered this when I upgraded.
For me, it was not a problem. I wonder if this is related to the message I'd sent to the two authors when I had tried out phpMyAdmin 2.6.0rc-1 which had a collision error between collections. (Collections are a character set encoding for your database table).
If the query or data is expected to be in a certain encoding, but in reality the database is stored in another, you will encounter errors. You encounter this when you load phpMyAdmin 2.6.0-rc1 for the first time and it tries to query the phpMyAdmin table for meta info. This didn't happen on the beta2 release.
Anyways, reverting to MySQL 4.0.20 prevents this potential configuration and data migration problem -- but be aware of it for the future!