very unlikely that you have damaged anything based on what you have stated so far. I will say some gear (especially DSS receivers) are sensitive to IR overload and depending on the IR repeater system you are using you may have the output set too high.

To test to see if you have an issue with the IR reciever in the DSS receiver, point the factory remote at the unit, if it works then move on to testing the emitter in different locations near but not over the IR receiver until it works properly, if you can control the output, such as if you had an MRF300 base station from URC then you may want to try adjusting the output.

If you are using an RF base station to do your IR repeating, then whatever you do, do not have the base station sitting on top of the DSS receiver, the microprocessor will interfere with the RF, and cause IR issues as a result.

hope that helps.