See OPs other post on withholding wages. http://www.expertlaw.com/forums/showthread.php?t=198200 to read more backstory
That said most employers have a statement in the handbook that states they reserve the right to revise the policies. So yes, they can update the policies at will. Your question needs to be is if they have to notify you prior to doing so? Prudent employers would get your signature on a new handbook/policy, but again it can depend on what you signed when you signed the original acknowledgement.
At this point I would suggest you take everything you have -- old/new handbooks, copies of any agreements to a local employment law attorney. Or like has been suggested in the other post, file a wage claim with the DOL.
I would also be talking with the new employer and asking when they were expecting to pay that penalty fee to the old employer. There are a lot of hazards for moving from a consulting firm to a client because there are 2 big players (the two employers) and one small player (the employee). You are getting stuck in the middle unfortunately.

