I presume that Options|MIDI Thru is checked, then there are two ways to "swallow" a MIDI message (and prevent it to be output to MT's MIDI OUT):
1) create a specific Translator entry to swallow the MIDI message
In this example, we want the MIDI message 90 40 7F to output a keystroke, and the MIDI message should not be forwarded:
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First Translator entry:
Options/General: Stop Processing: unchecked
Incoming: 90 40 7F
Outgoing: the keystroke
Second Translator entry:
Options/General: Stop Processing: checked
Incoming: 90 40 7F
Outgoing: None
The None outgoing action will take care of swalling the MIDI message. It's important to not check "stop processing" the first translator entry, otherwise the second translator entry will never see the MIDI message and it's going to MIDI thru.
2) Translate the MIDI message to another MIDI message
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Incoming: 90 40 7F
Outgoing: 90 50 7F
Output both incoming and outgoing MIDI message: unchecked
I know you have tried this, but also this solution should really swallow "90 40 7F" and only send "90 50 7F" to MT's MIDI OUT.
Now there may be one reason why Finale/Sonar is still seeing the original MIDI message: some MIDI ports can be opened by several applications at once. Now you must make sure that Finale/Sonar has NOT opened MT's MIDI IN port. Use a virtual MIDI port like Yoke or Maple to connect MT's MIDI OUT to FInale/Sonar's MIDI IN.
Let us know how/if that works.
Regards,
Florian