I don't think it was ever specifically mentioned in the series (the writers made a point of making all the technology appear mundane to the characters - much as how we view jet engines and mobile phones these days - so they never need to have a conversation which 'showcases' the FTL).
However, watching the sequences where FTL is used makes it apparent that it is an instantaneous jump rather than some kind of hyper-velocity propulsion. The BSG wiki goes so far as saying that FTL travel is sometimes called "jumping" - in fact, I remember them describing the Pegasus' escape from the shipyards as using a 'blind jump', which the characters emphasis as an extremely risky undertaking.
Anyway - since FTL travel is instantaneous, it is entirely conceivable that a navigation error can land you inside a mountain (or a sun, or even inside another ship). The next question is - how would a transponder be intact enough to keep transmitting through the rock?