Well... the reply system is default one from Vbulletin and I can not downgrade to lower versions of Vbulletin due to security issues.

Still I will check if some Mod or addon is there which can help us.

Also, changing URL colors may be possible in themes but I need to check that out too.

IN short, I will do what I can to fix issues. For time being, Sam suggestion of removing format can be tried.