However when I add the Plupload module which would allow me multiple files selection it breaks!
If this can't be fixed, is there any other alternatives similar to Plupload that I can use with CKeditor?
Use Insert module instead of IMCE
Check the module IMCE Uploader. It depends on IMCE and Plupload.
Besides that, It also provides the Plupload uploader as a plugin (in this module) to allow uploading multiple files at a time. If you want to use it, just select "IMCE Uploader - Plupload" the module list and enable it