I'm currently getting Thermal Foundation iron nuggets from an AgriCraft plant farm, but when inserting them into a Compacting drawer they just fill it up without actually compacting into ingots/blocks.

Inserting regular iron ingots into the drawer results in iron blocks, ingots, and tinkers construct nuggets, so there may be an oredict problem somewhere.

It depends on your mod collection, mod pack, and state of the ore dictionary. Certain ore dictionary registrations will cause a key to be shut down, because it's indistinguishable from something like "ingotAnyMetal", which would allow all kinds of illegal conversions. I know this is the case in AgSkies 2.

There's an internal blacklist and whitelist accessible through MineTweaker, which would allow pack authors to fix this on a case-by-case basis.

Aha. How does one go about accessing the black/whitelist using MineTweaker? (I'm making a wild guess here and thinking I want to whitelist TF nuggets?)

You would add a line like this to a minetweaker script file:
mods.storagedrawers.OreDictionaryWhitelist("nuggetIron");

There is also a blacklist by the same convention. Some people might want to blacklist gold nuggets, because Thaumcraft registers its gold coins as a nugget.

Okay, I added minetweaker and it seems the Thermal Foundation iron nuggets are listed as both ore:nuggetIron and ore:cropFerrarium, could that be the source of the problem?

Going to try whitelisting nuggetIron.

No such method. Compatibility is good and all, but documentation is really, absurdly needed here.

Okay, figured it. For anyone looking into in the future, the line is:
mods.storagedrawers.OreDictionaryWhitelist.add("nuggetIron");