Hi Mark, what a strange issue you have, let me help you with this.
Try to download again the HelloThemes and open the "app" folder, then paste the correct files of the HelloThemes folders to the same folders that you have on your magento folder on your server, then refresh the browser and chek if you have the extra option on your magento admin panel named: "HelloThemes". Do the same procedure with the Helloupload and then disable the cache. Also make sure to give permission of "riding" and "executable" to the files that you pasted on the folder of your magento server. I know maybe this are the same instructions that you have already done but there are no more secrets for this, woud be better if you can tell us wich magento version are you using, just in case.
Let us know what happened after that, thanks!.