It may be a glitch, or it may simply be a setting difference between MC25 and MC29 that is causing the problem. That is why I suggested you do a restore from the MC 25 backups onto MC 29. Doing a restore operation from MC25 will eliminate an MC settings difference as the culprit.
When you click on the progress bar and you said it takes three or four seconds to resume playing the track, that definitely is not right. I doubt that is settings related, but you never know. Regarding the cross fade - when you say it is not working, what exactly does that mean? It is simply ignored? Is the cross fade timing off?
There are checkboxes (see pic below) under the track change setting that will affect the behavior. At a minimum, disable the "use gapless for sequential tracks" as having it checked will effectively override anything you have set for cross fade. You should enable the "do not play silence" checkbox, because if sequential tracks have a long silence at the beginning/end, the cross fade will be crossing over in the silent range and effectively do nothing. For the third checkbox, I personally would enable it. If you're in the middle of the song and you manually skip to the next one, having it cross fade seems counter to the desired action (to manually jump to the next song).
I personally only use gapless for track transition since forever, but as far as I can tell from my brief testing of various cross fade settings to answer your question, it seems to work.