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You said "whenever I try to open a bdf or vhdl file," sounding like it happens every time you open these files. If it is only part of the time, you might be having the same problem I have. Sometimes the GUI will stall, typically for 10 to 20 seconds, but sometimes as much as a minute. Sometimes the GUI will freeze permanently. In either case, there is low CPU utilization and no utilization from the Quartus GUI process. The problem usually or always happens when I'm using an editor window. I can go days without a problem, but when the problem starts, it often happens very often.
I have reported my problem to Altera. It would be good for you to file your own service request for this.
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My problem is exactly this, I have reported it to Altera as well, hope to find a solution soon
edit: typo
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