I don't remember seeing them but I am fairly certain they are there. If so, it's probably the windings on a transformer or a choke. Probably when upgrading the kernel, the empeg chews a little more power than normal.

I wouldn't have thought that programming the flash would increase the current consumption that much though. Re-reading you say it's a UART based thing. In that case it's possibly the UART level converters drawing a little more power.