The clock accuracy definitely has improved. The clock appears to only have lost 2 seconds in the past three weeks since I installed the new board and reset the time.
As for the flickering issue, my clock was flickering constantly from the second digit through to the 6th digit making the time unreadable, only the first digit was flicker free. After discussions directly with email@example.com after sending them a video of what the display was doing, they isolated the issue to my second LED board. When this was bypassed, the clock returned to normal - though it looks funny with the second digit blank, and only displaying down to ten's of seconds. Once I get the replacement LED board, I will update on the result.
One thing I found that by using a different USB power supply, the flickering varied in frequency, but could not correct the problem. With your display only flickering between a certain value, you could try testing with a different USB power supply and see if that fixes your flickering issue.
Update: My replacement LED board arrived today and fixed my flickering problem. The clock has now been returned to its rainbow glory.