The “Domain” match preference in entry#1 won’t have any effect since you have a Regex in the additional URLs for that entry - Regex’s are always treated as an “Exact” match.
Not sure off the top of my head whether that alone will explain your issue but also make sure you’ve read Preferred entries and understood how they are supposed to work.
I doubt it will make much of a difference but have you tried the latest KeePassRPC version? Just in case the entry configuration changes there have fixed a bug we’re not aware of.