We have a similar problem. Here is a little history.
All the workstations in our company have a dual monitor setup. Most are equipped with nVidia Quadro FX 4500 or 4600 and 21" or 24" monitors connected using DVI-I (a few have larger size monitors, like 30", 40" or 52"). We deployed 64-bit Windows Vista SP1 around March 2008 with the driver available at that time: 169.39 WHQL (2008-02-22). At that time and until recently, everything was fine, display-wise. The only annoyance was that the nView utility was not available.
Around November 2008, we deployed a new batch of computers. Of course, the latest drivers were used: 178.26 WHQL (2008-10-15). Suddenly, we started having a wave of blinking monitors. I troubleshooted the problem and found that the blinking seemed to start after Windows awakened the monitors from sleep state (after system went to sleep, or simply at power on if the monitors were left on power save during the night). I found that disabling the affected monitor in Windows display properties and enabling it back right away made the blinking stop temporarily (not turning the monitor off and back on, this has absolutely no effect). Preventing Windows from putting the monitors to sleep also reduced the recurrence of the blinking during the workday. However, every morning, I had to run through the company to disable/re-enable the monitors everywhere a new computer had been placed.
This lasted a few weeks. As they became available, I tried newer driver versions, up to 182.08 WHQL (2009-02-26). But no luck, the blinking stayed. Then I noticed I got the blinking on the "older" computers as well if I updated the nVidia driver there too. This only affected computers with an FX 4600 installed, not those with an FX 4500. With monitors from the "Eizo" brand, we get blinking. With monitors from the brand "Dell", instead of blinking, we get artifacts. This is especially noticeable on vertical lines: they "tremble", as if looked at through hot air (like on roads in hot summers, or mirages in the desert, if you see what I mean). With monitors from the brand "Samsung", we also get artifacts, but usually more like colored pixels running in lines along the edges of the monitors.
The symptoms are different according to the brand of the monitors (blinking or artifacts) but they are always caused by the newer versions of the driver. Disabling/re-enabling the affected monitor always stops the problem temporarily. So far the only solution I have found is to install an older version of the driver. In my case, driver 169.39 WHQL (2008-02-22) and earlier versions do not have the problem; driver 178.26 WHQL (2008-10-15) and all newer versions up to 182.08 (2009-02-26) have the problem. I did not have any version available between 169.39 and 178.26 to test, so I can't tell for sure for those in between.
I hope this information can be useful to others (and maybe prevent them from wasting as much time as we did on the problem). I haven't tried uninstalling the Adobe Flash Player. It is true it has been updated as well between the two deployments.