Although not a conversion ("migration") issue, the phenomenon of UNNAMED REFERENCES is discussed, as far as I can tell, only in the big migration white paper. (In the white paper, of course, they are supposed to work.) Unnamed refs are file refs that, rather than being stored in the file refs place (define file references) are stored in or with scripts (?). These orphaned file refs are created each time you use the "specify file" script step (import, open, etc) - thankfully not when using "perform script/external script" step. On a network, specifying fmnet:/IP/filename.fp7 works properly (i.e., correct file, file's current found set), but using the wildcard "*" [asterisk] in lieu of an actual IP results in what Bailey Kessing reports above (i.e., correct file, ignores found set). On a single machine, everything works like a charm, so developers get to wait until testing on a network to discover this zany bug.
I am recommending to my team that any time they see that "specify file dialog" when writing a script to think of another way. To see this bug (or some variant) in action, write a send mail script and try to specify more than one file as an attachment. The usual dialog states that one or more files can be specified with the add button or by typing paths. Even with an absolute path (IP, not "*"), files simply are not referenced beyond the first one.
This is a HUGE bug that FM seems to want to treat as a migration issue. It isn't. Make a fuss so we get a fix soon!