I'd guess that you set up a lot of situations that end up in combat? Just stop doing that. Start having them get into situations that require the use of the other abilties.
The fact that you call these "secondary skills" seems telling to me. It says to me that you too think of comat skills as primary, and everything else as secondary. That combat is what the game is about. So it's no surprise that these abilites are prized.
In the game I'm currently running, the highest abilities are "Quick Wit" and "Cunning" and the like. But I don't just do intrigue and such to cause this, I also have situations that involve fighting and magic use, and...whatever. The result is that the players are increasing those statistics that make the most sense to what their characters are going through; which makes their advancement pretty even in all areas. The point is that if you balance out what the action is about, players will balance out their expenditures.
Note that if they don't use a combat skill in a session that it costs them double to raise it. The rules already give you a way to disincentivize lopsided spending. Think "conflict" not "combat".
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