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good point but bios time doesn't affect the time you choose in your os.
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Although you might not notice it in modern operating systems, that's not quite true.
Your motherboard has a real time clock (RTC) chip that is powered by the CMOS battery, which stores and increments time (to the accuracy allowed by the RTC circuitry).
The BIOS provides one mechanism to view and alter the time setting, but a modern OS will normally use its own system call to access the RTC. Your OS will read and control the RTC directly and can use protocols such as Network Time Protocol to get time from an accurate source and alter the RTC accordingly. Whether or not it does that depends on OS configuration settings. If not using NTP, you wil have to periodically correct the time yourself (and whether you do this through the OS interface or BIOS interface is up to you).
Some OS's expect to see the RTC set to UTC time (e.g. Linux, *BSD), and will provide their own absolute timezone correction. Windows usually requires the RTC set to local time as it applies timezone corrections differently.
FYI: Problems may arise if using two OS's on the same physical machine - e.g. you set the RTC to UTC for Linux, but then dual-boot into Windows and find the time is wrong, so you correct the time manually in Windows, then find it's wrong in Linux .... and so on. If there'a an option to interpret the RTC as local or UTC time, then it should be set appropriately to avoid such problems - most modern Linux distros provide that option but I haven't looked at Windows 7/8 recently.
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The time displayed in Stellarium's toolbar is your system time (whether that's local or UTC depends on your OS and configuration). However, if you set a different location in the
Location Window that displayed time won't change. You say you've fudged longitude, so I'm guessing you've already looked at that.
When I saw the problem description, I momentarily thought that it was a typical RTC in UTC/not local problem, but that doesn't seem right for two reasons: (1) when Stellarium's location is set to your current location then, regardless of what offset the RTC chip is using, Stellarium ought to behave according to the time it displays in the toolbar (but see Andrew's post above about Stellarium's timezone settings); and, (2) sunrise at midday doesn't correspond to the UTC-to-Mackay timezone difference (it's out by 2-3 hours).
The only other thing I can think of is a setting in
Sky and Viewing Options window > Landscape, where there's a check box entitled
Use associated planet and position. If checked, then when you change landscapes, the location will change to that which matches the landscape (e.g. Guereins, France). While this does show up in the location selection field (and therefore should be fairly obvious if you're trying to find the cause) the time displayed in the toolbar still reads your computer's system time.
I'm not sure how you set up Stellarium each time you install it, but you should double check whether you're changing landscapes after setting location/timezone, just in case that's it.
Edit: Started this post before seeing Kevin's last reply.