So it appears the problem is with UniqueConstraint vs Index(..., 
unique=True).

Test case: https://gist.github.com/4291461

On Friday, December 14, 2012 11:43:19 PM UTC-5, Michael Bayer wrote:
>
> its probably some subtlety to the data that's already loaded and how the 
> collection is being mutated - it's unlikely Flask has anything to do with 
> it.   There may or may not be some less-than-ideal or buggy behavior in 
> association proxy, or it might be a premature flushing issue, but if you 
> can come up with how to reproduce that would be very helpful.
>
>
> On Dec 14, 2012, at 11:38 PM, Donald Stufft wrote:
>
> Hrm. I'll see what I can do. Though looking at what you posted it works 
> for me with that too.. So the problem must either be with Flask-SQLAlchemy 
> or with my own app code.
>
> On Friday, December 14, 2012 11:30:57 PM UTC-5, Michael Bayer wrote:
>>
>> I've cobbled together a complete and simplified test case given your 
>> mapping and example code and I cannot reproduce with either 0.7 or 0.8 - 
>> the count of rows in the association table is one on the first commit, and 
>> two on the second.
>>
>> You need to adapt the attached test case into a full reproducing case so 
>> that the specific trigger is illustrated...thanks.
>>
>>
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