Had this exact issue with my Multiplus-II 48/3000 about eight months ago. Drove me absolutely mad for weeks before I tracked it down.
The culprit in my case was the tail current setting in VE.Configure. It was set far too high — I think it was at the default 4% — which meant the Multiplus was interpreting the battery as "full" well before it actually was. Dropping that figure down to around 1–2% (depending on your battery chemistry and capacity) made an enormous difference.
A few things worth checking:
- Absorption voltage — is it actually set correctly for your cells? LiFePO4 wants something in the 54.4–56V range on a 48V system, and if it's set low the charger hits the ceiling too quickly
- Absorption time — are you running fixed or adaptive? Adaptive can behave oddly with lithium if your BMS is doing any current limiting
- Battery temperature — if you've got temp compensation enabled on a lithium bank, it can pull the target voltage down unexpectedly on cooler days
My bank is Fogstar Drift 280Ah cells in a 16S configuration with a Daly BMS, and the interaction between the BMS current limiting and the Multiplus's adaptive absorption was causing all sorts of grief. The charger would see the current drop (because the BMS was throttling) and assume the battery was full.
Worth installing VRM and having a proper look at the charging curves over a full day — that's what finally showed me exactly where things were going wrong.
What battery setup are you running? That'd help narrow it down considerably.