When you press Y over Pokemon Pearl, which game code does it display?
Looking at the XML, these are the ones I'm finding for Pokemon Pearl over various regions:
[E]: APAE EBEA12FB
[J]: APAJ D245F56D
: APAE 31D0AFDE
[K]: APAK 70453525
[D]: APAD AB50EC89
: APAI 8F21639A
: APAS F5737DD4
[F]: APAF C89A40B6
The first party loader generates a file with the rom name, appending a .cc extension. The second line of that plain text file will be a game ID as one of those listed above.
Provided that it's displaying APAE as it should, try rebuilding your cheat database by Y (Rom info) > Y (cheat menu) > select the Rebuild button. Otherwise, you'll have to manually edit your cheats by hand. Either edit CHEATS.XML and switch the tags to force it to recognize the region's list, or edit the .cc file.