After you rough up the end of the cell, wipe it off with something like motor apray to remove anything thats not compatible with solder. I use a cutoff wheel on my dremel and make a light pass over the end of the cells to rough it up, then wire it clean with motor spray and a clean rag.

You prob should be using a separate rosin core compatible flux if the solder is not wetting the surface of the cell. That cleans and preps the surface for soldering, sometimes the flux in the solder is not enough. After cleaning, keep fingerprints of anything thats going to be soldered, the grease in fingerprints can mess things up. I use an 80watt Weller to put together or repair pacs, it does a good job.

Pre-tin the end of the cell and the batt bat, that way you'r en the cell for the minimum time possible with the heat. If you put too much heat into the cells, you can compromise performance.