I was looking at the category rules for the class% categories, and I noticed the rules seem to contradict themselves regarding whether the timer should be stopped or not while moving between maps.

For example Ranged Assassin% Category Rule 3 says "We want the runner's ability to be assessed, not your computer, so pause the timer as soon as you give the last hit on each Nexus of the 3 phases". But then Rule 5 says "The timer doesn't pause in between maps". So I'm not really sure how to determine the run time.

I also noticed that the Support% Rule 3 is different from the other class% Rule 3s - it doesn't contain this sentence about runner's ability, but all other class% category rules do.

Sorry for the confusion, I'll fix it.
But already answering your question, it is to pause the timer between matches.

I just fixed this, I removed the extra language from Rule 3 and changed Rule 5 to the below, for all current full-level categories except the Veteran Intro. Although come to think of it perhaps that category should be changed too, to the sum of in-game time from the frame control of the character is gained to the frame the victory condition is met, for each of the 3 stages (requiring re-timing of all existing runs for the category).

"5. The time for the run is the sum of in-game time taken across all 3 maps. If necessary, ties will be broken by timing frame-by-frame across each map, from the frame the timer hits 00:00 (no negative sign, i.e. the frame the gate opens) until the frame the core hits 0%. Unless there is a tie, do not time or report to this precision."

Nice Freeze, thks