The length of your stroke is all about your torso rotation. It has nothing to do with your hands. IMO when you change your feel on the paddle, or anything really, it opens up the opportunity for mental lapses in technique. Why? Because if you're focused on what's changed with your gear, you can not focus on running the river.
Many people's technique for dealing with this is to paddle only with what you are used to, but then when you get something new you just have to gut it out until you can get used to it. A better solution might be to relax your mind and focus on the river, instead of that your pogies feel weird. I only bring this up because Rivervibe was asking about his stroke length in relation to the pogies, which IMO are not, and can not, really be directly related.
I personally like pogies, mainly because when my hands are cold I wear'em but when I enter a rapid I generally take them off and slide them to the middle of my paddle. I like to be able to have my hands available for rescue, grabbing onto rocks etc., so for me, pogies offer the most flexibility. If it's really cold though this technique yields fairly cold hands. I have an old pair of Mountain Surfs and refuse to give them up because they are the shortest cut out there and very easy to slide your hands in and out of.
Cub boater: "What do the spiders mean?" Old fart boater: "Trust your intuition." CRCII