I have an xbee pro talking to another. I can transfer data, but data goes missing from the stream. Why?

I have an embedded controller hooked to my GUI over a serial link. I can transfer ASCII data just fine, but if I transfer data that is not ASCII (random characters 0-0xFF), I lose data over the link.

Is there something that removes characters from the link?

No the XBee modules do not offer that kind of function. What xbee modules are you working with and what settings do you have on them?