Can you redownload from
http://cit.cohtitan.com/downloads/SentinelPlus.tgz
And see if it still happens in the latest build?
Edit: The spaces in folder name issue should be fixed in this version also, or so I'm told. 
diff says there's a difference, but I don't see what it is. Line endings or something silly? I haven't broken out the hex editor yet...
Will send the results to you again.
Two suggestions, neither of which are really that important, but would be nice:
1: Put a version resource in so Get Info shows the version number, etc.
2: I've lost data because it overwrites files. Either generate a new name ( file-1, file-2, etc) or warn and pop Save As instead? Or just abort, but that's annoying too.
The second may be a feature; you may want updates to be easy, and that may be right.