There can't be any connection between the number of selections active for auto-trading and the time it takes to refresh a market, unless:
a) You have turned this setting on: "Retrieve all price offers"
b) You use a particularly complex formula in your trigger that affects the time needed to process one selection. I'm talking about a formula comprising, say, 100 parentheses.
Otherwise the program makes exactly one call to BetFair to get the data for all selections in one market, regardless of whether the selection will be traded or not.
If you attach your settings file, I can take a further look at this problem.