Question and partial answer - may be helpful to some readers.
I use HMRC's own online filing software (as agent), as I only file a handful of very simple Self Assessment tax returns.
I had problems because the page where you are supposed to be able to view, save and print a tax return would not generate a pdf file of the return, so I had nothing I could send my client. (The 'black and white' version is no good as it is far too complicated for my clients and doesn't look like a return.) The system would not let me view, print or save anything at all.
I rang the Online Filing helpline and they told me it is a problem with my Internet Explorer settings. To solve it they told me to:
1. In Internet Explorer, go to Tools...Internet Options... Advanced
2. Scroll down the list to the heading 'Security' and tick the box for 'Do not save encrypted pages to disk'. Click OK.
3. Close and re-open Internet Explorer
4. Log onto the online filing system again and you should now be able to view, print and save a pdf file of the return.
HOWEVER this pdf file of the return does not include the 32-digit unique reference that is required to identify the version of the return that you are submitting (it appears on the 'black and white' summary but not on the pdf return). Therefore even if my client signs a copy of the return, in principle I cannot tick the online declaration that will allow me to submit the return.
I rang the Self Assessment helpline to query this and they told me that at present there is no online solution to this. They said I should hand-write the version reference onto the pdf tax return and ask the client to initial next to it (as well as signing the return as normal) and return the form to me. Presumably if sendingn the pdf file by email I can ask them to copy the reference number onto the return themselves, and hope they get it right!
A further problem remains, in that the on-screen page from which the declaration is ticked and the return is submitted still shows the name of the agent ,not the taxpayer, at top right. The Self-Assessment helpline told me that this problem has not yet been solved. However since the return itself is clearly in the name of the taxpayer I suppose this is not really a problem.
So my online filing difficulties seem to be solved or worked around - for now at least!