The issue on "popup disappear and then reappear" is fixed in the latest Development version 9.0.374.0 or later, please take it to have a try.
For new question, I guess you can give a right-margin to the element added to the popup's content to work it around. Hope it helps.
BTW, would you please create a new thread to post these issues related to marker's popup? in that case, it should a bit easier for others to track it.