500 Internal Errors (no replies)

We've recently been getting a lot of 500 Internal Errors. We really thought it was a programming error or something but speaking to my hosting company, it seems that Piwik is causing some visitors to receive a 500 Internal Error.

On the error_log file under the piwik subdomain we get this error about once a minute:
PHP Warning: Module 'pcntl' already loaded in Unknown on line 0

but sometimes in the same file it also says:
Error in Piwik (tracker): The Piwik URL https://analytics.****.com/index.php does not seem to be pointing to a Piwik server. Response was ''.

I'm having a pretty hard time figuring out what the issue is.
I had an htaccess file setup to disallow visitors from the Piwik login page. Could that possibly be what's causing this.
The .htaccess file is:
<Files "*">
order deny,allow
deny from all
allow from MY IP
allow from MY IP
</Files>

<Files ~ "^piwik\.(js|php)|robots\.txt$">
Allow from all
Satisfy any
</Files>

Any idea what could be causing this?

Thank you in advance for your help.