I found a bug about takeovers. I had a train assembled in depot. Then I merged companies - the train belonged to the company that ceased to exist. Now that train cannot leave depot - saying no route.
New trains can leave depot just fine, old trains that were on tracks can be sent to depot and dispatched again. I tried to dissasseble and reassemble the train, that did not help. I have bought new engine, and attached old cars to it - it dispatched OK. But old engine with new cars didn't go anywhere. So the problem is only with engines (either powered vehicles or first vehicle in convoy). Debug save: http://list.extended.simutrans.org/~simutrans/debug-saves/depot-after-merger.sve
Look for Gosish train depot of Great Beltwell Railroad (yellow player) and the Class 91 in it.
Thank you for the report: I believe that I have now fixed this. I should be grateful if you could re-test in the next nightly build.