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Now one question. In steps 1 and 2 you are doing the exact same thing for the exact same device. why would quartus ever not be consistent?
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Experience :)
Quartus should *always* give the same synthesis result given identical files and an identical start seed. However, some versions of Quartus break this consistency as shown in my PCIe timing analysis tests;
http://www.alteraforum.com/forum/showthread.php?t=35678 The advice to repeat step 1 as step 2 is a good sanity check :)
Ideally you would synthesize your design via Tcl scripts, that way there is no ambiguity as to whether or not you repeated the synthesis steps exactly.
Cheers,
Dave
Honored Contributor
