See the following (or also the section "Importing V3 Profiles" in the help file):
viewtopic.php?f=29&t=9643
Basically V3 uses a non-Unicode filename format in the Zip files, but V6 uses Unicode (so that it can store filenames in any non-English language). They aren't compatible which is why, if you keep using your old V3 Zip files, you'll have problems, e.g. the same file could appear twice in the Zip file (once in non-Unicode format and once in Unicode format).
When you install V3, or import old V3 profiles, you'll get a warning if any profiles are using compression.
viewtopic.php?f=29&t=9643
Basically V3 uses a non-Unicode filename format in the Zip files, but V6 uses Unicode (so that it can store filenames in any non-English language). They aren't compatible which is why, if you keep using your old V3 Zip files, you'll have problems, e.g. the same file could appear twice in the Zip file (once in non-Unicode format and once in Unicode format).
When you install V3, or import old V3 profiles, you'll get a warning if any profiles are using compression.