Repeated reference pattern issue

I'm having an issue with performing repeated patterns on a quilt.  Unfortunately I can't share much due to confidentiality so will have to do my best to describe.

I'm starting with a 'base/origin' quilt on which I perform a number of patterned merges.  Usually I model another quilt which is to be merged, copy that quilt, pattern the copy, merge the first copy with the base quilt (ensuring the base quilt is selected first), select that merge feature and select pattern which would automatically detect the previous pattern and do a reference pattern of the merge.

However on this particular model this works once but when I try and do it a second time, the pattern feature button is either greyed out or the pattern instances are overlaid in a single point (seems to vary when I've fiddled around to get around the problem). If I create a copy of the base/original quilt and merge with this instead, the second reference pattern works fine (as do subsequent patterns but a copy of the base/original quilt is required each time) but there are fairly major disadvantages to not being able to carry a single quilt/feature reference through the design process.

From what I've managed to find by googling there seems to historically have been some issues/bugs with reference patterning. My general understanding is Creo sometimes struggles with which previous pattern to reference if there are multiples.
Is anyone able to clarify this for me? Is there a reliable way of making it clear/isolating which pattern is to be referenced? Any help would be greatly appreciated.