If you are using OllyDbg, I suggest installing an anti-anti-analysis plug such as ScyllaHide. For ScyllaHide, grab the latest from the releases and follow the instructions in the ScyllaHide.pdf document. Then you can try the various techniques simply through a set of checkboxes.
Generally, if you suspect that a particular anti-analysis technique is being used but your mitigation technique is not working, then you should check for that anti-analysis technique manually. To do this with IsDebuggerPresent, or any other API call, go to the function (in Ollydbg, ctrl-g and enter "IsDebuggerPresent" without the quotes) and set a breakpoint (F2 for software BP, or right-click -> breakpoint -> hardware) on the first instruction or any instruction before the first branch (e.g. jmp, conditional jump, call). Sometimes the program will check for a change to certain APIs or skip over the first few instructions.