In my experience the taxman is stamping down on people who set themselves up as self-employed and work for only one company. There's nothing wrong with a limited company doing work for only one company.
Alex, I'm with WWW on this one. I have run my own limited company within the aviation industry for the past 9 years and income from one client is viewed as improper. It is seen as the client evading the costs of employment and the limited company using company tax breaks (what few there are left) to avoid personal income tax. That is certainly the view of a learned Counsel and my company accountants.
HWB