Hold on guys; that thread is long and covers a lot of ground. The primary issue and several related issues were fixed in X3. There remains one issue that I know of that a MIDI track that has focus while another track is armed to record will show a false "confidence recording" indication as described above, and if looping is enabled, can actually cause playback on the wrong instrument on the second and subsequent iterations of the loop.
That may be part of the problem being described here, but some of the other symptoms don't align with that.
In any case, in order to troubleshoot something like this and have a chance of other users replicating it, you need to boil the project down to the minimal configuration that demonstrates the issue, and very thoroughly describe all of the routing, port and channel assignments, input echo status, etc. of all MIDI tracks and MIDI Out enabled synths in the project, and the MIDI configuration of the controllers (e.g. does it have a MIDI In, and does its MIDI Out act as a Thru?) and MIDI interfaces.
At this point, the description of the problem is way too sketchy to make sense of.