I also have a Mk4 I use with WINUAE and it works wonderfully but I did have problems knowing which dosdrivers to use on the amiga side.
First:
I remember reading somewhere, think pretty resently on amiga.org in the news section, that some of the newer 3.5 inch floppies are not dual speed and cannot access DD disk with catweasel. It suggested using an old 3.5 floppy drive, like an older teac.
Second:
I suggest getting mdisk362 from the individual computer site. use a text editor and check the dosdriver files and make sure it is configured properly for amiga disks, HD and DD require different dosdrivers. There are examples in documentation somewhere on the individual computers web site. Make sure you know which position on the floppy cable the floppy drive resides.
Third:(using the catweasel with WINUAE)
I know that newer versions of winuae do not need MS windows drivers but will use them if present, try the ms windows drivers on individual computer site, CWMK42200.zip. Not only may this help you on the amiga side but ver 42200 has some very cool new formats for convertion.