I agree with your approach.
With that said, I have a strong filling that timing isn't the trouble maker in this case.
Just completed the following test:
Step 1. On a PC with V14.0 I compiled the design and converted the SOF file to JIC (on the same V14 machine) - design works.
Step 2. On a PC with V13.1 (same source files) I compiled the design, converted the SOF file to JIC - design doesn't work.
Step 3. I took the SOF file generated from the PC with V13.1 and converted it to JIC on the PC that runs version V14 (the PC from step 1) - design works.
Clearly, the issue here is the SOF -> JIC conversion process when done on the V13.1 machine.
However, the file conversion settings are absolutely the same on both PCs!
Unless it's a Quartus bug - I'm really baffled...
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And as with most of my IDE frustrations - this one also ends with a simple google search.
http://www.cubiccyclonium.org/support/kdb/solutions/rd10162014_566.html