does Protractor not work well with Mechjeb?

[lyndonguitar]

I've been using both for some time now and I noticed that most of the time, When I try to use protractor or at least the kerbal alarm clock launch window planner, and then Launch on that specified window, using the "transfer to other planets" does not seem to work together with it. It tells me to wait like xxx more days(ranging from a few days to even a year), even when protractor already says it's time to launch.

it's like mechjeb computes for it's own launch windows.

It's not a problem though because I could just follow either of the two but has anyone had the same experience as me when trying to use both?