I'm running a number of mods and can provide a list if needed, but I don't think any of them are to blame - save, perhaps, in having added a number of items to the game. I am running with the alt-key to move stack option on.
Succinctly: I'm transferring all of my assorted cache of weapons, fighter LPCs, cargo, etc. from my primary colony planet to another one. The first stage of this process is, obviously, loading everything onboard. Everything, in this case, consists of about 30+ rows of assorted goods, weapons, LPCs, blueprints, and various special goodies. After about 17 rows the interface begins to lag, and after about 20 it lags very badly. Finalizing the transaction fixes the problem, and it doesn't return except when moving that many different kinds of goods hither and yon again. I'm guessing that there's something going on in the list of goods that are getting moved that gets recalculated every time something new goes in that ends up scaling very badly, exponentially so, at high numbers.
Not sure if a fix is worth dev time or if I've simply stress tested Starsector's market interface, but I thought I'd put it out there.