I have had a look at the top level assembly on my machine and I am able to see the assemblies updating straight away no matter what configuration I use. Have you ran the SolidWorks RX tool to see if there are any issues with your system? It may also be worth checking to see if your graphics card drivers are up to date, this can be done through the RX tool or the SolidWorks website.
I tested this using SolidWorks 2015 SP3.
I've ran RX tools and I had to update the video card driver, but that does not solved my problem.
I have SW 2015 SP4.
Tested on one of my colleagues computer with the same bad results.
I don't think it could be a video driver problem, I will try to make some print screens to better explain how the assembly wrongfully updates.
Thanks for your effort to help!
I've marked on print screen some bad positions of parts/features.
Note that the subassembly detects no interference, only when used in the top assembly there are (many!).
I suspect it is somehow related to the layout sketch that I have used to drive the assembly, with configured dimensions.