Lee, I think that it isn't the mentioned pump issue, as that would be a constant and this problem is not.

Thomas, the next flight did not flame out, at full power or otherwise, so I don't think I am making bubbles due to any leaks. I am inclined to retain the filter but will perhaps tap/shake it occasionally to see if micro bubbles are accumulating there.

Thanks for your inputs, hopefully I can experiment more on Monday.