Had this exact issue on my boat last summer. Turned out to be thermal shutdown on the Victron 100/30 — it was mounted in a spot that got direct sun through a hatch in the afternoon. Moved it somewhere with better airflow and it sorted itself out completely.
Worth checking a few things:
- VictronConnect app — hook up via Bluetooth and check the history tab. It'll show if it's been throwing thermal or overvoltage warnings
- Panel voltage — if your panels are getting very hot mid-afternoon, Voc can actually drop enough to cause weird behaviour depending on your setup
- Input voltage — are you near the top of the controller's rating? Hot days can push things oddly
Also had a mate with a similar symptom that turned out to be a dodgy MC4 connector on the panel side. Intermittent connection, showed up worst when the cable expanded in the heat.
What controller model is it and what's your panel config? Makes it easier to narrow down. Also worth posting your VictronConnect screenshots if you can grab them during the dropout — the data logs are genuinely useful for diagnosing this stuff.
Not uncommon on boats either where ventilation is rubbish and everything runs hotter than it should. Is your install in an enclosed space?