Has anyone continued having this problem despite switching Mail software?
My mail is grouped 100% correctly online on Google Mail.
However on all email apps it was mixing up my mail.
I started on Spark then moved to another 3rd party Mail app, then tried Apple's own, and this issue was still there.
It led me to look at what is the constant between all the software. I nailed it down to the system clock.
My system is grouping messages incorrectly because I run my system clock +12mins fast (sounds silly but its beneficial to me to feel like Im constantly late...). So the system time doesnt match the 'real' international time, and it creates a weird vortex of mixing up groupings and email trails in incoming and sent messages on all of the applications.
Reverting my system clock to the 'set time and date automatically' setting resolved the issue across all software.
Hope that helps someone out. Was driving me crazy.