I'm not sure exactly what you're trying to accomplish with the CTCSS plug-in. Is it simply to help identify unknown signals or are you trying to use it for actual tone squelch purposes? Again, in either case, the aforementioned KGTone will do either job until and unless this issue is resolved. It's free software and it can even handle processing audio if you simply pipe the audio out of SDR# via a virtual audio cable (some of which are free as well). It also does an admirable job of decoding DCS as well, along with DTMF, and if it is legal in your area, it can do a fair job of unscrambling some voice inversion. In my opinion it is worth a try for anyone who wishes to accomplish any of this.
I read the comments at RR as well and it doesn't seem as though it will be fixable in the short term, anyway.
Scott - KC1UA
Marstons Mills, Cape Cod, MA USA