I suggest that you try the following:
Use a configuration files for all your settings, that will make it more easy to troubleshoot

Make a file called, something like "miner280x.conf":

{
“pools” : [
{
"url" : "stratum+tcp://yourrpool1.com:3334",
"user" : ".",
"pass" : ""
},
{
"url" : "stratum+tcp://yourpool2.com:3333",
"user" : ".",
"pass" : ""
}
],
“intensity” : “20″,
“vectors” : “1″,
“worksize” : “256″,
“lookup-gap” : “2″,
“thread-concurrency” : “32765″,
“gpu-engine” : “1000″,
“gpu-memclock” : “1350″,
“gpu-powertune” : “20″,
“temp-cutoff” : “99″,
“temp-overheat” : “95″,
“temp-target” : “90″,
“expiry” : “120″,
“failover-only” : true,
“gpu-threads” : “1″,
“log” : “5″,
“queue” : “1″,
“scan-time” : “60″,
“scrypt” : true,
}

Then called the miner with:

cgminer.exe -c miner280x.conf"


Try to exclude the enviroment setup to begin with so you you only call the miner with your configuration file.

The following should force your GPU to i high clk freq:
 “gpu-engine” : “1000″,
“gpu-memclock” : “1350″,

- If you get the same result (or simular) try to decrease intensity (I know that a 290X should be able to run i = 20, but just for the trouble shot)

Report back

Try uninstalling then re-installing the catalyst driver, unchecking all other weird programs it tries to install (including the catalyst control center), only selecting the VGA driver if possible.  Then run gpu-z to see your clocks, or afterburner to try overclocking.