In any scientific sphere, if you find an effect you then want to find a mechanism.
If caps do sound different then there can only be a number of explanations:
1) The caps are different value.
The most likely explanation. Few people measure the capacitance before fitting.
Wez's finding with the ceramic caps is interesting; ceramic caps have a poor reputation, but could this be due to their very poor tolerance?
2) The caps are distorting the signal.
Capacitor distortion can be measured in electrolytic and polyester caps. You would never use the former as tone caps. Polyester caps show a signal dependent distortion; however the effect is only measurable at the sort of signal levels you would find in a valve amp, and even then it's debatable whether this is audible.
If you use polypropylene caps then distortion is not an issue.
3) Series inductance.
This could affect the tone response, but only if the series inductance were large enough. The series inductance however is very low for caps, and this, in my opinion, is unlikely to have any audible effect.
4) Some other effect that has eluded scientific investigation.
I would put this in the unlikely category.
I think Wez hit the nail on the head with this, ie you need to measure your caps before installation.