This reminds me of a school project (building a sound card) where I noticed that when I plugged the oscilloscope at one point it changed the output at another point --> I threw out the board and decided to never do hardware again..
If the probe was single ended (e.g. not a differential probe or handheld unit), you may have shorted something to ground without realizing it. Was a long time before I figured that one out.
Nope it was a differential probe. I suspect that we broke something in the board when plugging the probes..