Laerion,
Can you answer some more questions for me to understand the issue better ?
1) Whats your build id. Copy paste it from Help > About MyEclipse Enterprise Workbench.
2) Do you have any third party plugins installed ?
3) Is your HTML/JSP file very huge? Is it a simple web project ?
4) Clear the .log file which is located at <workspace dir>/.metadata/ .log. Perform a clean. Here is an FAQ for clean :
https://www.genuitec.com/forums/topic/troubleshoot-using-the-clean-command-line-argument/
5) Now check if you are able to replicate the issue. Check the .log file for any errors logged. Paste them here for me.
Let me know how this works for you.