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You can try changing it in cvPCB to the actually available TQFP32 footprint.
Can you tell us which KiCad build are you using?
Maybe the schematic symbol has a footprint assigned by default which does not necessarily correspond to the name of the actual footprint in the footprints library.
What is in your fp-lib table?
Maybe the bug you're mentioning is related to your situation.
I'm pretty sure the schematic symbol for the ATmega has a footprint already assigned. In the schematic editor right click on the symbol and select Edit component>Edit.
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