This is interesting to me because I have had something similar happen most recently (just prior to disassembling my Amiga).
I was worried it's an image corruption.
for me, the situation is this:
A500 with V500v2+ using CFCard/SD adaptor on the IDE controller of the Vampire.
I got a wrong block ID error and ran PFSDoc. A ton of errors, same as you posted (Allocated but not used) and I think all of them were in WHDLoad/Games drawer.
As soon as my Amiga is back together I was going to install a fresh image of ApolloOS r43 (the one I am currently using that gave me errors). Once I put the fresh image on the system I will immediately run PFSDoc before any errors appear to see if it's a base image issue or something else. I haven't checked my buffers. Will have to wait until my A500 is up and running again.
Very interested in your outcome.
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