As AvaTar mentioned before - run the debugger on that bootloader code (or LED toggle code) and see what happens. You will need to figure out how to tell your IDE to NOT "run to main" but instead allow you to single-step from the reset vector.
Also, check the option bytes using whatever programmer you are using, specifically the "user configuration" bytes. Is it possible that when programming the custom bootloader that somehow the option bytes got changed to enable one or more watchdog timers? Or change the boot selection options? I don't THINK this is your problem because the reset period looks the same as your first scope screen shot. But these are (or should be) easy things to check.
Also check the brown-out reset voltage in the option bytes and make sure it matches whatever power supply voltage you are using.
Otherwise, double-check for some kind of power supply issue. Is the 2.2uF cap you added/changed still attached with good solder joints?