At pH <4.6 it is of no use talking about F0s. I would be more inclined to look at hot filling and sealing. If you cannot control the fill temps adequately then you can still heat process the product after sealing. I would look for a schedule that achieved a temp of about 90 degrees in the product. This would make it more than safe. To achieve an F0 of 3 at 103 degrees, this must have been a very very long cook time.
You have not actually mentioned what the flavour change is, is a bad taste or other. If you could be more specific it may help identify the cause.
One possible reason may be if you are using a lot of spices is that the spices are continuing to add to the flavour profile over the time in the package. This is not unusual for sauces or chutneys/relishes etc for this to happen, in many cases it is desirable.
One way around this is to use spice oils, as they do not continue to add the flavour once fully blended into the product. Another, it may or may not be possible, is to steep the spices in the sauce during the cooking process and then remove them before packing. The way I do it in my home kitchen is to tie the whole spices etc into a muslin/cheesecloth bag, place this in and cook until I am happy with the flavour, then remove the bag and throw it in the bin. Like I said I do not know if this is a possibility in your process, but food for thought.