surely it was the fact that i did not have my 3dskybox covering the whole of my original map and just covering what i had made for the skybox.
Please rephrase that sentence so it actually makes sense. Also, as a personal request, please put in spaces after your full stops and commas, your bad grammar is driving me nuts, not to mention making your already poorly structured sentences difficult to read.
Assuming you actually meant that your 3dskbox did not match the size of the original map; The size of the 3dskybox will not cause the game to bug out like this. Be it too large or small in regards to the scale of your original map area.
But there probably was an issue with your 3dskybox. Possibly an invalid brush or improperly setup entity (sky_camera?), miss textured brush face etc. Or that you simply missed a leak warning in your log. 3dskyboxes can leak, and do for people frequently. People frequently forget to add in a floor to the 3dskybox for example, under a displacement, or some such oversight. They are tricky things to master.
I can't say for sure though without seeing for myself, and discussing it after you resolved the issue is kinda pointless now (though i find it important people understand where they went wrong so that they may avoid it in future). Just that i seriously doubt that was actually the cause of this error. you just inadvertantly fixed it by doing one thing that could have resolved any number of issues (by removing the offending objects altogether); and drew the wrong conclusion from the result of that action, despite the fact it worked.
I'm just glad you have it working and can manage to avoid this again in future.