Something else to consider is the effect of the scope probe itself on the circuit being probed. The little bit of capacitance of the probe can change things, especially if you're working with higher frequency circuits.

One problem I was searching for on the backplane of a mainframe computer would always disappear when I probed it. To make the problem stay away while I looked for more serious problems a 10 pF "virtual probe" was placed on the signal...

Dennis