Ok I will try and clear things up a bit (again). My 'outrageous speculation' of structural problems is not speculation at all - it is in the public domain.
News article about repairs work prior to first flight, this was due to de-lamination observed during the static testing performed in 2008:
No verdict yet on completed tests to 787 wing repairs - SmartPlanet
Note the quote "The aircraft did go to limit load as intended" however at that point analysis was still ongoing. I certainly haven't found anything more recent about the results of the test. It is possible to perform the first test flight even if the results were not that favourable (after all you are not going to come anywhere near limit load on your first test flight), but the authorities will almost certainly ask you to demonstrate that the flight envelope is being limited to mitigate the risk.
Flying at reduced weight and limiting the types of manoeuvres performed can help limit the envelope, particularly for structure where the critical load cases are the manoeuvre load cases, but for areas driven by gust cases it can be much more difficult to protect in this way. In fact adding ballast in the wings can help mitigate for this by increasing inertia and providing some bending relief. Another way to protect for the gust cases is to keep the wing inboard loaded to reduce the bending moment.
Now maybe you can understand why my observation that negative aileron deflection (yes negative means up - thats the convention) may have been employed to inboard load the wing. This would reduce the bending moment at the root joint and hence the load at the crown fittings (these are effectively transferring the bending moment into the centre wingbox structure as a couple of two running loads - compressive at the top skin joint and tensile at the bottom skin joint.) If you reduce the bending moment you reduce the load on these fittings.
I am not suggesting there is any new problem, just that the use of load alleviation may be a symptom of a well known existing problem, and was wondering if anyone had any 'information' that might better explain the aileron position at takeoff. You will note my post title was "signs of trouble ahead?" not "signs of trouble ahead!" There is a very big difference.
I am in no way trying to belittle the achievement - the 787 is a beautiful aircraft, and a revolution in systems and structure design and manufacture, and will certainly be a great success. My question was really around whether the use of alleviation suggests that there may be further delays before first delivery, or if there is another explanation.
Note that I do not think the wing deflection is a design flaw - it is a design feature, and a beautiful one at that.