HTTP/PHP Processes Killing Server

I have recently moved my WP website from a subdomain to the top domain of my vps. Everything was working just fine on the subdomain, but right after i have uploaded database and files to the public_html folder i have noticed multiple php processes “eating” 100% of the process.
I started to investigate and tried few things, like dropping database and re-uploading it, erasing all plugins (from db as well), erasing all files, but nothing worked as on subdomain (i did changed all the paths in the db file accordingly).
I had to google for the problem, after seeing some of these php processes were looking like this:

write(4, “\275\3SELECT t.*, tt.* FROM wpone”…, 193) = 193
read(4, “\1\1\n=\2\3def\voneshopp_db\1t\rwpon”…, 16384) = 743
access(“/home/user/public_html/wp-content/themes/compare/footer.php”, F_OK) = 0
time(NULL) = 1354130656
lstat64(“/home/user/public_html/wp-content/themes/compare/footer.php”, {st_mode=S_IFREG|0644, st_size=1450, …}) = 0
lstat64(“/home/user/public_html/wp-content/themes/compare”, {st_mode=S_IFDIR|0755, st_size=4096, …}) = 0
lstat64(“/home/user/public_html/wp-content/themes”, {st_mode=S_IFDIR|0755, st_size=4096, …}) = 0

And found like a solution to replace wp-includes/http.php with a modified version. By doing that i actually reduced my vps load from 15 to 0.25, some of the php processes were still there but they were not consuming that much cpu.

Obviously, the http.php version i’ve uploaded was incorrect, i ended up with Fatal error: Cannot redeclare class WP_Http in /home/user/public_html/wp-includes/class-http.php on line 34

I had to place back the original WP 3.4.2 http.php file.
Does anyone have any clue about the cause of the problem i’ve encountered after i’ve moved the WP site from subdomain to a main domain (basically from one folder to another) ?

Any suggestions, ideas on how can this be fixed is highly appreciated.
Thank you.
Laguna