Just left my host for a similar issue, Arvixe shared Linux server. One of the shared users apparently installed some utility called siteapps, which some how effected my side of the server, not certain what it all does but it started showing 'badges' on all my pages saying 'this site has been optimized by siteapps'. I found a way to turn that off in cpanel but the siteapps was still injecting JavaScript code into all of my pages. I could not see any visual changes to the pages but found this unacceptable.

I tried to contact support only to find out the company had been sold recently and the new owners saw fit to fire all the support staff and do away completely with telephone support for technical issues. Tried chat and after waiting, no joke, three hours for someone to show up in the chat was told that the problem was with my code. Even after telling the agent I could upload a blank page and the code would be injected into the page.

Long story short, I am now hosting on my own server. Now looking for a good host I can point my customers to, one that won't try to nickle and dime them like godaddy.