Strange happenings there mate which I've never seen before. Suggest you Flash the Firmware and do full Re-install of Mach3 and the Plug-in.
Make sure your running as Admin.

The number for filter is 1, don't go anyhigher as it slows the input reaction times down. It works like mach3 noise filter. Never had to use it yet thou so can't see why you would unless you have a wiring issue some where.?

Regards the Spindle Fault Output then hard to say without seeing how you wired it. What VFD and are you using Relay output for fault or Digital output in which case then both VFD and IP-S will need to share the same Ground Ref.