Due to a build script bug the rt-c64-0801.h file looked like this:

#pragma cc64 0xfd 0xfb 0x801 0x824 0x9ce 0xa000 0xa000 tmp/rt-c64-0801

Namely, a tmp/ in the library name param.
When running tests with that, compiling this line with cc64 led to a CPU jam in VICE.
This doesn't seem to have anything to do with VICE not finding a file but is more likely either due to a parse error in the param, or due to a buffer overflow.