hmm...did some tests..
...loaded the single specpls3_flop.xml as datfile in its own profile....no issues in rebuilding and scanning
...imported MAME .162 plus the single software list ""...it's not listed in systems at all...most likely because the list is not named correctly in the hash file...it's using "spectrum_flop" in there and a single import tries to run MAME with data export of "specpls3_flop". ...so blame MAME devs for this ;-)
...imported MAME .162 plus ALL software lists...worked fine...(since it does not run single data exports then)...assigned a sysdefpath for it pointing to the previously rebuilt sets....no issues...no warnings...normal scan duration.
so...sorry...no issues here...
....regarding the last test I forgot to say that I only enabled THAT single software list in....maybe it's some sideffect with other ones....so you might give that a try, too....sorry that I can't help more at the moment due to lack of time
besides of this....you may prefer the one-xml-as-one-profile mode, so you got access to all software lists separately (and could use the batcher to run a scan/rebuild sequentially).