If you have a display or lights on the bike that are powered by the battery, and those remain on when the controller cuts out, then it's probably the controller LVC.
Some controllers have jumpers on the board inside to set it's LVC. Others are programmable, if you have the right software (from the manufacturer) and cable. Others are automatic, and set their LVC when the battery is connected, so if the battery is at a voltage near the "border" between two set points, the controller might set itself to the wrong LVC. No way to know what those set points are, however, without experimentation, on any specific controller.
If they turn off when the controller cuts out, it's probably the battery shutting down due to cells dropping below LVC under the load (especially if this controller pulls more current than teh old one). Leaving the battery on the charger for days (or weeks) anytime it is not in use may correct this, at least temporarily.