Answer:
One difference is that the treaty had a much more diplomatic conclusion in mind than the joint resolution. The treaty was an agreement that the US would go and negotiate borders with Mexico so they could gain the territory that would soon become Texas. However, the joint resolution was actually a declaration of war on Mexico with the goal of obtaining Texas, which was vastly different than the "talk it out" idea in 1843 (the votes in favor of this in congress was also greatly influenced by a recent event during April of the same year where Mexican soldiers crossed the Rio Grande and killed 11 soldiers, but i digress)
Another difference is that the treaty was opposed by Congress since it would give the slave states a political advantage and they didnt want to change the balance of free and slave states. The joint resolution wasnt opposed because the US was angry at Mexico for killing their soldiers so yeah
Hope this helps :)