Doing some extensive testing on this - SPELLLEVEL CLASS=... does not work under the Pathfinder game mode at all. No spells display in any capacity.
It does work under the 3.5 game mode however (just loading 'basics' for testing purposes.
Comparing the 3.5 to the PF classes file, there are only a couple of differences;
Pathfinder has MEMORIZE:No, 3.5 does not
Pathfinder uses Arcane Bond. 3.5 uses Summon Familiar (not anything to do with SPELLLEVEL, just mentioning it)
Adding Adept=# in the spells.lst file does work as a work around for now (not commenting out the SPELLLEVEL in the classes files has no effect btw)