Quartus GUI doesn't match QSF

[Altera_Forum]

When I pull up the Quartus GUI, settings reflected under the "Assignments->Settings" window do not match what is in my project .qsf file. Here are some observations that I have made: 

• In the "Analysis & Synthesis Settings", the "Timing-Driven Synthesis" option is selected. 
• In the "Fitter Settings" under "Timing-driven compilation", "Optimize hold timing" is selected and set to "All Paths" 
• Even though I observe that the following settings are set in the GUI, the SYNTH_TIMING_DRIVEN_SYNTHESIS and OPTIMIZE_HOLD_TIMING values are nowhere to be found in the QSF. 
• Additionally, the timing optimization advisor is telling me it might that it would be a good idea to enable the "Optimize holdtiming" value to "All paths". 

  None of this is adding up to me. Has anyone else observed behavior where the settings specified in the GUI are not reflected in the QSF?  Note that I observed this on a Linux box running QII 10.0 (no SP1).

[Altera_Forum]

are you able to move to 10.0sp1 or even better yet 10.1sp1? 10.0 had a decent number of GUI problems like this

[Altera_Forum]

I am...it just might take a few days as I don't have control over my machine...not ideal in an engineering environment...thanks for the heads up...I suspected it might be something like this...

[Altera_Forum]

Those are defaults(definitely TDS, but not sure about Optimize Hold Timing). There are a ton of assignments, but if you start a new project you'll note that the .qsf is almost empty. Only as you go to non-standard settings do they appear. (I believe is something is already in the .qsf and you change it to a default, it won't get removed). So, for example, if you want to see Timing Driven Synthesis show up, turn it off in the GUI, save the project, then turn it back on and save the project.  

(It can be annoying, but I've seen old versions where every possible assignment is listed. There's a reason it was disabled, as everyone complained...)

[Altera_Forum]

Funny!But i can not understand that

[Altera_Forum]

As Rysc points out, the .qsf file will contain any settings that are changed from the defaults. The default settings are defined in the .qdf files. There is a Quartus II install .qdf, and there can also be a project .qdf. The .qsf settings override the project .qdf settings, which in turn override the Quartus II install .qdf settings. If you want, you can change the defaults settings by modifying these .qdf files.