I also fail to see obvious memory leak issues, so maybe it's time for some paranoia:

1. use strict; use warnings;
2. protect against pathologic filenames and use the 3 argument form of
   open(UNMODIFIED,"<","$processedDirPath/$matchingFiles")
   (good style, but unlikely to be the problem)
3. my bet: add a size check like

   -f "$processedDirPath/$matchingFiles" and -s _ < 40960 and 
       do{warn "size or type problem with $processedDirPath/$matchingFile
   +s\n"; next};
   [download]

4. idle curiousity: there won't ever occur further STRUC20 alone or as part of something else after the first occurance?

Update:

• what do you mean with print DATA!? These changes don't touch your copying loop at all.
• anyway, the size testing goes before your open() calls, that is: in the outer loop.
• btw, consider rename instead of mv.

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