I was just typing in a bug report for this same “issue” but the brilliant forum platform immediately flushed out this post. Mickey: Thank you for responding with a workaround.
Going back to my monkeying I see the contextual F3 hooks in the ‘lost’ pattern. Cranial adjustment to old thinking?
I cautiously say workaround, as it’s not intuitive; There are now two processes for adding a repeat on adjacent/sequential pattern entries… Do this on every ‘other’ pattern, it behaves as the OP, and I, and flow would dictate. On sequentially looped patterns? New process.
I create a Song, repeat-press F2 after selecting an initial pattern, and pop pop pop the consecutive patterns slot in. I wish to repeat (using 10 to 16 eg.) 10, so cursor on 10, F1, and default is repeat, press enter, get 2X, enter again, pattern 10 is ‘wrapped’ in the loop.
Here’s the confusion. If I then go to Pat 12, F1, Repeat 2x as before, it ‘loops’ just that pattern as with 10. NOW, if I go up one, to Patt 11, and do the exact same, I get what the original poster gets… a repeat is added up into the above ‘already-repeated’ patt, follow with length (2x) and enter, and this ‘open’ repeat drops back down above my current selected pattern and does nothing. Pressing F3 on the pattern, repeat catches into place, and having a fiddle I see how F3 operates. “I accept that at this point, this is how it is.” But…
Wouldn’t it, for repeatability’s sake, make sense to have the same behaviour when inserting a repeat on any given step that a moment ago was done a different way? Should not adding a repeat, be a repeatable process for simplicity? not change if you’re against another sequence? leaving the F3 key intact of course too?
Like the OP, I was just stuck there… Alright, I should have pressed the Help/0 key perhaps?
This is two processes for the exact same procedural step… isn’t it? If I’m missing the reasoning, I apologise. I’m not in a smoking jacket with a brown and yellow synthersizeur at my side writing this mind you… coughing on sherry and ceegars.
On 10, add a repeat. Makes sense.

Do the same on patt 11, repeat is inserted up into the above… confirm 2x, and enter, it then looks like the dangly one.

If “that’s the way it is” with a proverbial grin, I humbly accept. The S2400 is a great studio machine to get things done, having had an SP-12 back in the 90’s and based my songs on pattern lists in the song mode. Other sequencers were crap, and my Linn Sequencer, and Linn 9000 always crashed. This has been really fun to go back to, from eMagic’s later wreckage that ended up the de-frocked Apple Logic.
I’ll turn pattern repeat off on myself now, and leave my two bits to dangle here. Access to product devs this readily is nasty… but appreciated. Thank you.