Splatter, I just racked a beer a couple of days ago, and the initial ferment was very vigorous, and I think the bubbler on the 2ndary carboy has moved, well, I don't even know... it has lifted up, so it's had something through it, but I haven't actually seen it bubble. The brown ale done before that bubbled reasonably steadily for about 3 days... Anyway, if what you moved has come out smelling and tasting like beer, relax. Leave it to condition a week or so, then take a SG and see what has happened. At any rate, don't worry about it.
Did you take a gravity reading after primary? Just about every beer I make is fermented out before I even get a chance to rack to secondary. Secondary for me is more of an aging/sedimenting phase where my beer gets a chance to "brighten" up a bit more before going into the keg. If your gravity is near where it should be, you're fine.