You are experiencing those erratic behaviors because custom descriptors are still being applied. After unchecking the Custom Descriptor property, you should also delete from the WebContent/WEB-INF/descr folder of your project the .descr file matching the Id of your page.
For example, if you are disabling custom descriptor of Page page123, be sure to delete WebContent/WEB-INF/descr/page123.descr. If you are not using custom descriptor anywhere, you may safely delete the entire WebContent/WEB-INF/descr folder.
What are Custom Descriptors
Descriptor files, found in the WEB-INF/descr folder of the generated application, contain the logic that drives an application at runtime. Normally, WebRatio automatically generates those files from your model.
By enabling Custom Descriptors your are beasically taking charge of "generating" those files manually. This is a rather hacky feature that should be needed only in rare circumstances.
The WebContent folder of Web Projects is used to specify a set of files and folders that are copied over the generated application. When first enabling custom descriptors, the customized and "frozen" descriptor file was subsequently being copied over, blocking any automatic update by WebRatio. This is exactly what the warnings were telling you about and the reason you has to manually delete the descr file(s).