Messages in this thread are quite old but since I had the same issue and found what was wrong in my system I thought I'll post here as it may help somebody else.
In my case problem was in wrong permissions of
/assets/components/phpthumbof/[b]cache[/b]
.
After spending some time snooping around I found that after "Clear cache" in admin is clicked, there is an ajax call sent to:
/connectors/system/index.php
In /connectors/system/ directory I found nice error_log (error log location can differ as it depends on server config) with info:
[09-Mar-2014 13:20:06 America/Toronto] PHP Fatal error: Uncaught exception 'UnexpectedValueException' with message 'DirectoryIterator::__construct(/home/user_account/public_html/assets/components/phpthumbof/cache/): failed to open dir: No such file or directory' in /home/user_account/public_html/core/cache/includes/elements/modplugin/3.include.cache.php:50
Stack trace:
#0 /home/user_account/public_html/core/cache/includes/elements/modplugin/3.include.cache.php(50): DirectoryIterator->__construct('/home/user_account/...')
#1 /home/user_account/public_html/core/model/modx/modscript.class.php(66): elements_modplugin_3(Array)
#2 /home/user_account/public_html/core/model/modx/modx.class.php(1541): modScript->process(Array)
#3 /home/user_account/public_html/core/model/modx/processors/system/clearcache.class.php(26): modX->invokeEvent('OnSiteRefresh', Array)
#4 /home/user_account/public_html/core/model/modx/modprocessor.class.php(173): modSystemClearCacheProcessor->process()
#5 /home/user_account/public_html/core/model/modx/modx.class.php(1631): modProcessor->run()
#6 /home/user_account/public_html/core/model/ in /home/user_account/public_html/core/cache/includes/elements/modplugin/3.include.cache.php on line 50
Changing permissions to 777 (chmod 777 cache/) solved the issue for me.