is there some other step to trigger the bug?
I've packaged up a reduced system. http://ashby.csail.mit.edu/abcl-obo.tgz
Unpack, cd into the unpack directory, and execute bin/abcl Once loaded:
(setq obo (make-instance 'obo :path "~/Desktop/abcl-obo/unit.obo")) ;; adjust to where you unpacked it
#<OBO {E71A6D}>
CL-USER(8): (read-obo obo)
Debugger invoked on condition of type JAVA-EXCEPTION: Java exception 'SchemeException: ERROR: NO INSTANCE METHOD OF TYPE
(.matcher org.armedbear.lisp.Cons ...)'. Restarts: 0: TOP-LEVEL Return to top level.
If you evaluate the read-obo function and try again it will succeed, demonstrating that the compiled version doesn't work as compared to the evaluated version.
Similarly if you disable the inline lambda expansion and recompile it will run without error.
-Alan