Problem with iMessage contacts being separated by phone number and email

Question

Hi all, sorry if this thread is a duplicate of another, I've seen some that are similar but none seem to match the exact situation I'm having.
Me and 3 other friends have a group iMessages thread where we talk to each other.
We each have several devices: ie. I have a Macbook Air and an iPhone 5S, one has a Macbook, an iPhone 4, and an iPad, etc etc. Essentially we all have a mix of devices which we can use to read the thread, all using the same Apple ID and with our phone number added.
The problem is, every so often and for no discernible reason, someone will send a message and it'll start a new thread: this usually happens on my iPhone but occasionally it happens on my Macbook. Sometimes, what has become 2 threads on my phone will be only one thread on my Macbook, and vice versa. Same applies to my friends. However, sometimes what has become 2 threads for them is still only one thread for someone else, as though some of us have gone "out of sync".
When you compare the contacts in the 2 threads, they are IDENTICAL (can't stress this enough, the contacts themselves have not been duplicated), however when I look at the same contact from one thread, their phone number will be highlighted in blue. In the other thread, their email address will be highlighted in blue.
Therefore the problem seems to be that devices are unable to bring together an iMessage sent from a contact's phone with one sent from their email. If the information for both email and phone number are correctly filled in for a contact, why can Messages/iMessage not realise it is the same person and bring them together?
The problem is, sometimes a message sent from the same device will first be sent from the phone number, then the next will be from the email address (or rather, everyone else's devices are seeing it that way, they're not doing anything different than usual, just typing in the thread and pressing send). Its as though the device is choosing one then the other, seemingly at random, and iMessage doesn't seem to be able to add them to the already existing thread but instead creates a new one as the "source' is different. Is this behaviour intended? Surely it can't be.
Is this something to do with the "You can be reached by iMessage at" setting in iOS. One of us needs to be reached by both his email and phone number so we can't just all turn off the email on our phones/iPads for example.
Is this a known problem? Is there something we can do about it? Is it ever going to be fixed?
We've tried other messaging programs but they're just not as well integrated as Messages, and obviously being able to switch between my phone and my Macbook is hugely convenient.
Any help would be much appreciated, we're now at the stage where we have 2 iMessage threads and a backup LINE group chat for when things are completely unfollowable due to every other message going to the duplicate thread.
Thanks in advance.

Answer 1

When you go to Settings>Messages do you see your Apple ID at the top?  Also, when you go to Settings>Messages>Receive At do you see both your email address and your phone number listed?