The bootstrap utilities (m.i. the bootstrap compiler) are not influenced by the fpcupdeluxe version.
Fpcupdeluxe reads the Makefile of FPC to find a bootstrap version.
FPC 3.2 contains this:
REQUIREDVERSION=3.0.4
REQUIREDVERSION2=3.2.0
FPC trunk (3.3.1) contains this:
REQUIREDVERSION=3.2.0
REQUIREDVERSION2=3.0.4
As you can see, version 3.0.4 is allowed for both 3.2 as well as 3.3.1.
However, 3.0.4 does not work that well anymore.
If fpcupdeluxe finds an available 3.0.4 in the bootstrap directory, it will use it while it is allowed by the Makefile.
If you delete the bootstrapper, fpcupdeluxe will download a new one. The highest allowed. So, it will try to download a 3.2.0 bootstrapper.
So, deleting the bootstrapper and re-run fpcupdeluxe might solve this problem.