Communication with bluetooth module

I'm trying to create a project that communicates with a bluetooth module (Sparkfun BLE Mate 2) over UART. The module scans for peripheral devices and reports a list back to the computer over serial, basically straight from the example code in the library. Problems arise when I try to scan for devices over and over again in void loop. I eventually was able to scan multiple times by reseting the module every time, but only the very first scan reports the correct MAC address of the periphery devices. Subsequent scans report corrupted MAC addresses (probably about 80% correct characters). I believe it may have to do with leftover junk data being left in the Arduino buffer, but I'm unsure how to proceed or if that's even the problem. I should mention there is a kind of multiplexing board being used, also from Sparkfun, that allows the Arduino UNO R3 to communicate with the computer or the module using the hardware serial. Every time it changes, a serial.flush command is issued.
Any guidance towards properly using the buffer and serial communicating with the module would be very much appreciated!

Without posting your code how can you expect us to help? Please use code tags

so it looks like this

Also, please post links to the datasheets for your Bluetooth module and any other extra hardware you are using.

...R