I seem to remember a situation with one of my employees, it happened a long time ago so I cannot remember how it was resolved, but my employee was given a deduction by accident. This deduction was made after taxes had already been made on the employees pay. I was happy to put it right asap, but of course by paying it back it meant the employee was going to be taxed on it again as it showed in the pay before taxes. I gave it to my accountant to deal with and it was resolved. You need to check if the original deduction was made after taxes. If so, you have effectively been taxed twice. If this is the case and your company cannot sort it out, I would contact your local tax office to see what you need to do.
Hope this helps, with the other issues, I would just make a nuisance of yourself until your pay is corrected. Legally this is your money and they should put it right immediately, not make you wait until they feel like sorting it out!