Sir,
According to Section 66 E (e) of finance Act, 1994 " agreeing to the obligation to refrain from an act, or to tolerate an act or a situation, or to do an act" is a declared service and liable to service tax. In your case liquidated damages are deducted from your bills for the reason of not meeting the specified performance level of the equipment's supplied as well as the delay in supplies. This amounts to tolerating an act or a situation. Therefore liquidated damages are amenable to service tax.
Regarding availment of credit you have to satisfy the authorities in what way the service tax paid on liquidated damages satisfy the definition of 'input service' which is used in promoting your business. You may say that payment of liquidated damages improves you efficiency in manufacturing quality goods or providing services without any complaint from your customer. This you have to decide before availing the credit. This is my opinion.