"I just built a jump ship and can't get it to transit. What's wrong?"
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There are several things that commonly go wrong here:
1) The size (in HS) of ships that can transit a JP is the
lesser of the capacity of the jump ship's jump engine and the size of the jump ship itself. In other words, if you build a jump ship with a 6000 ton (120 HS) jump engine, but the size of the jump ship is only 5750 tons (115 HS), then it won't be able to escort a 6000 ton cruiser through the JP - the biggest such cruiser would be 5750 tons. Note that this limit is on a per-ship basis; the jump ship could escort 2 5750 ton cruisers as easily as one (assuming its squadron size limit isn't exceeded for a combat transit - see below).
2) Ships with non-civilian engines (i.e. military, GB, fighter) cannot transit a wormhole created by a commercial jump drive. The technobabble for this is that the commercial wormhole pays for its higher capacity with a lower stability, and would be destabilized by the transit of military-grade engines with their higher power levels. So don't put military engines on a commercial jump freighter
Commercial ships can, of course, transit through wormholes created by a military jump drive.
3) If you've given a "squadron transit" order to a TG, then the number of ships in the TG (including the jump ship, but not including embarked parasites) must be less than the "Squadron Size" parameter of the jump drive, and the jump ship must be in the TG making the jump. For "standard transit" orders this is not a problem, since the standard transit order tells the jump ships to open a long-term wormhole through which any number of ships can pass, but which disrupts their sensors etc. for a longer period of time. So for the jump ship and two cruisers discussed in #1, the squadron size of the jump ship's drive would need to be three or greater.
4) Note that when you're doing a squadron transit with multiple jump ships, the Squadron size is
not cumulative. In order to fully utilize the squadron size ratings of multiple jump ships when doing a squadron transit, you must break the TG up into multiple TG, each with one jump ship. This is because the wormhole created by a jump ship in a squadron transit appears in a random location on the far side of the jump point; different jump ships (and the ships they're escorting) will come out in different locations and so can't be part of the same TG.
5) For experienced players: Steve took out the checkbox that turns jump drives off on ships - he said it was doing more harm than good. So this is no longer a failure mode.