REWRITE: Ok rewriting this to make it clearer.
I have created a custom module using this (http://www.silksoftware.com/magento-module-creator/). It works fine however I needed to expand the module after i created it.
I went into my database, went into this modules custom database table, added the required entries and then from this generated the create SQL, I went into the module and added in 2 more text fields that were required, updated the database create in the install to reflect the new structure, uploaded it and cleared the cache. However it did not update the admin side.
I then recreated the module in the tool linked above, as an update with the new SQL I just generated as an update, with the new fields. and uploaded this (note this has worked repeatedly for me before on my other modules). Uploaded this and cleared the cache like I usually would and it did not work once again.
I then tried again with the tool with a much higher version number just to see if this would force the update, it did not work.
I then started faffing about, deleting the core_resource row, clearing the cache, deleting the VAR folder, uninstalling the module then re installing it from a base 0.1.0 with the new fields.
However no matter what I do once I pop the module files back onto my site the site just remembers the old structure and shows me that.
I also tried disabling the module before deleting and clearing the cache, then when re installed the module is re installed as disabled. so it's not being fully removed.