I have a 16 gb wifi ipad jb with jailbreakme.com i installed backgrounder and skyp. When i close skype and background enabled it goes to wait when i open it again it resumes.
The reason is that the latest version senses for home key and power key press. Once you press the home key to go to another app, Skype automatically puts you on hold. Same works with the sleep button. Previous version as mentioned should help.