Initial entry into UK on ILR visa & subsequent trips abr

I am a UK citizen living in the states & my wife is Japanese. We previously lived in the UK as a married couple & my wife has ILR status but we moved to the USA & have lived there nearly 10 years. We are now returning to the UK & I am applying to get her ILR status back as a returning resident, which I hope shouldn't be a problem. The issue is that following our entry back into the UK (likely in June 2010) & subsequent activation of her ILR status, my wife would soon like to go on a summer trip (say 4-6wks) back to Japan, after which she will return back to the UK. Would this be ok or could she face problems entering the UK from Japan given that her trip to Japan was so soon after she entered the UK as a returning resident. Thanks for any advice on this.

This might not be as easy as you think...

You may return to the UK as a resident if:

1. you were settled in the UK when you last left; and
2. you have been away for two years or less; and
3. you are returning to live here permanently; and
4. you were not given public funds to pay the costs of leaving the UK.

When did she last travel to UK on her ILR and have any steps been taken to keep her ILR active by regular trips here?

Also:

If you have been away for more than two years, you must apply for permission to return (known as 'entry clearance'). You should apply at the British diplomatic post in the country where you live now. The entry clearance will take the form of a visa or an entry clearance certificate.

After moving to the USA, we did return to the UK every year which kept her ILR active, but have since been out of the UK for more than 2 years so need to reapply. I was told at the UK Border on our last trip that this would be straighforward as she was previously a resident & is married to me (a Brit!), so we have just submitted the application to the UK Consultate in New York to get this back in advance of our relocation in June. My question is really more focussed on when she enters the UK (assuming our application is successful) as a returning resident, will it cause a problem that she wants to leave for a holiday in Japan within a couple of weeks after entry into the UK, or won't it matter (ie. the return within 2yrs rule will just simply kick in)...?

It shouldn't matter, but it reads as though she will be holidaying on her own, so she should be prepared for questions at immigration along the lines of "Where is your husband now" and "Why didn't you travel together?" - routine stuff, shouldn't trouble her.