So after receiving an e-mail from someone asking whether I'd heard anything more regarding the TFS Merge issue I blogged about a while back, I checked a post on the VSTS User Education blog that I had previously left a comment on regarding this issue.
There hadn't been any follow-up, but upon taking a look at the referrals associated with my original post I noticed some originating from forums.microsoft.com. These referrals took me to this thread that talks about this issue (and included a link to my post, hence the referral).
The long and short of it, is that this appears to be a known issue the 'debit/credit logic within Merge' , which based on the last message in the thread appears to have been fixed.... something to look out for in the forthcoming RC.