After feeling that Timer Balls were a bit off while playing on a multiplayer server, I decided to set up a test area in a single player world.
Setting in a spawner that generated level 1 Lickilicky in creative mode, I did several experiments. Lickilicky were chosen for their catch rate of 30 which makes them unlikely to be caught initially, but allowing 100% catch rate when dropped to 1 HP, put to sleep, and with a timer ball counter of at least 9. I achieved with a level 100 Parasect with false swipe and spore.
After various tests using abilities, items, and thrown balls, I repeatedly encountered fights where the capture would fail even when it should have been 100%. As far as I can tell, it seems that throwing a timer ball early in the fight freezes its counter, causing all future timer balls to use that same ball multiplier, even as late as thirty turns into the fight.
I'm not sure if this triggers on all ball throws, or just timer balls, but throwing a turn 1 timer ball, then waiting 9 turns before throwing another would frequently result in failed captures on sleeping, min HP Lickilicky.