After years and years of experience, with similar stuff happening on my equipment, I'd recommend that you check the simple stuff first.
- Did you swap connector #1 and #2? (Sounds stupid, but I've seen it done)
- Cleaning the connectors could have bent one of the contacts. Make sure all the solder connections are good, and that the pins are straight.
- Is there anything that could be shorting the signals to ground? (I've seen cases where one strand of wire comes off the connector and contacts the shield, or the ground. This will cause some really interesting results.)
- With all the moving and bending involved with taking a connector apart and cleaning it, it's possible a connection has been broken. Or if not broken loosened, creating a cold solder joint. This will raise the resistance of the connection, which would change the amplitude (and possibly the shape) of the signal going across the connection. One way to check for this is to Ohm the connection out. Anything above 1-2 ohm's is kind of high, but compare the results of each pin to the others in the connector. If they are all pretty much the same your probably good. If one is dramatically higher that is the culprit. It docent take much of a change in resistance to have a big change in a signal.
Hope this helps a little.
Jason
P.S. I'm a big believer in the "Smoke theory"
There are several theory's about how electronics works. The smoke theory states that: Electronics will work fine until you let the smoke out!