After doing some searching I saw that this is in fact the case. To overcome it you are supposed to upload your apple touch icon in the “Default & Custom Icon Pool” area of the WPTouch settings, and then select your uploaded icon in the next “Logo Icon // menu Items & Pages Icons” area, in the “Logo & Home Screen Bookmark Icon” select menu.
The trouble is that the “Upload Icon” button in the first settings area is dead: I click it but nothing happens!
But I noticed that the blurb contained the note, “These files will be stored in this folder we create: …/wp-content/uploads/wptouch/custom-icons“. But I took a look and saw that no such directory had been created! So I created it myself, and FTP’d my icon into it. Then, voila! My icon was then available in the “Logo & Home Screen Bookmark Icon” select menu. But what a palaver – why doesn’t the upload button work in the first place ?