There's several reasons they can do that, and possibly more I don't know about.
The first is that the games could be encrypted to a different GP32 ID or SMCID than the one you're using them on, in which case - naughty naughty
- but who'd do a thing like that?
The second (and more likely) is that you've flashed your bios, and when you registered the GP32, you did it in the PC-Link mode in Pacrom; in which case the ID that Entware got would be wrong (on ID request, pacrom just gives either 000000000000000000000 etc. or FFFFFFFFFFFFFFFFFFFF etc.). If that's the case, you'd normally have to re-buy the software. Thankfully, Entware is run by a load of human beings rather than a load of computers, so if you give them an email (its sure to be somewhere on their site) and ask them what to do, they'll help you out. If you're using mr_spiv's combo firmware then you can get the proper ID in the PC-Link bit of the official fimware using GPS2. If you're using some other one, then there are a few programs you can get (or so I'm told) that tell you your GP32 ID by running them. Or you can get the official bios in .gxe/c, .gxb, or .fxe format (no idea where, but I know it exists).
If neither of these describes your current situation, get in touch with Entware and see what they say... they'll probably be able to offer better advice than I've given