Exact same problem here with X-T3 grip. I rarely remove the grip from my camera since early 2019. Always fully tightening the grip to the camera whenever possible. Put batteries only in the grip (except when updating firmware). Mostly charge batteries in the grip.
The grip start behaving strangely 1 month back. Initially, boost mode were rapidly activated and deactivated without touching the boost mode switch. Then comes battery indicator issues. The issues were initially infrequent, then worsen within last week. Coming from X-T1 with VG-XT1 and never had any problems, I checked few things on the newer cameras:
1. Got small portion of dirt on my camera contact pads. Cleaned it and trying to attach the grip straightly seemed solving my problem. It seemed okay to tighten the grip, though not too tight that might damage the mechanism. X-T3 (as well as X-T2) grip pads are somewhat less spaced than the X-T1's. Dirt build up might lower the impedance between pads, hence either the "short circuit" or bad contact.
2. Prior to X-T2, fuji cameras do not communicate with the battery. They just sense the battery level by its voltage. Only 2 battery contacts are used in both X-T1 and the grip. X-T3 and X-T2 communicate with the battery (possibly uses serial signal), and might rely on it to determine the battery level (hence displayed value in percent). Once the communication disrupted (by dirty contacts or so), battery level reported to the camera might be off. In my case, I only put 2 half charged batteries in the grip, LCD shows 3 batteries, all red. But strangely one of them is 100% instead of depleted. The next time I restart the camera, it would ON for just 1 second, no battery indicator shown, then turn off by itself.
