Oh, I didn't know you were adding a bacteria supplement. I also think that is behind the smell. When I get bacteria blooms in my tank it smells like a stagnat lake. XD You are probably smelling dead bacteria because it's hard for bacteria to survive in a bottle with no light at room tempurature. You won't see a stable cycle in a 2.5 gallon so there is no point to the bacteria suppliment even if it did work. Once you leave out the suppliment the smell will probably go away. :)
Just to be nosy, Since you removed the sand are you going to use gravel or have a bare bottom?