I have the similar problem.
I updated fpc 3.2-fixes (rev. 4138) and lazarus trunk (rev. 60458) and now I get "Error: the Fppkg configuration is corrupt."
Please see the attached picture.
Even more strange is that:
Lazarus 2.0-fixes does not have this problem when compiled with this fpc 3.2-fixes.
Lazarus trunk does not have this problem with fpc 3.0.4
Only the combination of Lazarus trunk and fpc 3.2-fixes.
Might be important to say that I do not have .fpc.cfg in my user folder, but each fpc version has its own in <fpc_install_folder>/lib/fpc/etc/fpc.cfg.
My system - Linux Mint 19.1 xfce 64-bit.