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let me tell you that all seems to be working as expected or as long ago (maybe not so intelligently:) designed.

in a nutshell: there's these simple xml session files (.qtr, .qts); there's these even simpler session template files (.qtt), same as previous but without any media content, and then there's these full-bundle session archive files (.qtz) where everything goes into one single zip file.

which one you use is at your disposal. iow. it's an user option, and that's precisely the one you take while you do a File/Save As...

otoh. all media filenames are prepended (prefixed) with the session name (cf. File/Properties...) which is not always the same as the session file name. can you see the difference? i hope so ;)

anyhow, but not particular to the point, i'd also recommend you to a more recent version if you can--0.5.5 is way too old anyway, one year+ is a lot of time already.

hth.
cheers