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Found the error.
Compare Thri-Kreen Weapon Mastery with Valenar Weapon Training.
First the rules text, then the XML implementation (just so you can see they should be identical, but are not:
The wording in the short descriptions:
Gain proficiency, +2/+3/+4 (by tier) to damage with...
Testing in the old character builder, it appears to me that Dwarven Weapon Training lets you get your +2 to damage when using a hammer as an Implement, but Thri-Kreen Weapon Mastery does not give you +2/+3/+4 to damage when using a Gythka as an implement. I am too tired to rules-wrangle, can...