If the cells are way out of balance....it'll take a while to get em back to equal. You may not be seeing the cell 2 light blink as it's the one that's under-charged so the balancer is only pulling juice from the loaded cell.
If it's only reading one cell upon initially plugging it in, either the pack or balancer might be damaged. If possible, try to borrow or use someone elses lipo or balancer to try and isolate your problem. If your LHS is worth its salt, they should be willing to help you diagnose the problem as well, without spending a bunch of dough on stuff you don't need.