How to get the planned dates that make sense on replan with timesheet entry

If we have a validated start date and duration, when you first create the activity with auto planning ticketed. It takes the start date as the planned date (ie. validated start and planned start are the same and then calculates based on duration and availability the end date for the activity, plus availabity of assigned resource from the validated start date.

No.
Planned start date is not the validated start date, unless you select planning mode "must not stat before validated start date".

There will always be activities which we wish to plan in with out a dependence and not start at the very beginning of a project which could be months before, todays date.

If the task does not start at the beginning of the project, there is a reason, and IMO it is a good option to define it with a dependency.
OR possibly you can use planning mode "must not stat before validated start date"

If the person has not recorded time on timesheet then the planned start and end dates must not change with a re-planning of project.

It may in many ocasions :
- if resource is also assigned to new activity with higher priority
- if planned start date is passed and real work not entered (so task is late...)

We found before the upgrade that if when re-planning we used the project start date which could be in the past it would leave the independent activities where nothing has been recorded as actuals with no changes to planned start and end dates.

If no other new constraint changes the availability, you are right.
And this has not changed since many versions (at least V5.x)

If some time has been recorded but not all time assigned in a timesheet then I would expect the planned start date to reflect either the original planned date or the real start date. The re-planned end date could then be based on the duration of the activity and availability of resources from the start date.

The duration is used for planning only for planning mode "fix duration". All other modes don't care about duration.

Do I need to raise this a bug? Enhancement, I really do not have to make a decision that projeQtOr is not workable with time sheets it would loose a lot of the benefits of using it.

I'm afrait I don't understand what you call a bug.
What you describe seems for me a normal behavior.
Real work follow up and it's planning need to follow up the rules of effort driven capacity planning.
Planning is calculated to take into account constraints, availability and real work.
It will not always reflect what you want it to show, it will reflect the reality.

Maybe if you can describe (possible with screenshots or drawing) what you get (which data on which screen) and what you expect to get, I could understand what you need.
Also to understand what you get, I would have ot know the planning mode of your activities.