Hi queenoffreak, getting a little unclear here as to your activities. All items being removed from view in eBay when you first join Auctiva is a one off, the indexing delay happens everytime from a 3rd party site including Auctiva.
However scheduling from eBay costs money and of course if the listings are already on eBay early enough it is quite likely they could index them ahead of them actually going live, henec no apparent delay. This is obviously not possible when they arrive from a 3rd party site.
You as the seller of your wares need to determine which is best for you based on your wares and customer base as to which route for listing is best for you, e.g. that paying eBay for scheduling is insignificant relative to your planned profit.
As an aside, the delay does not affect end time and most bidding in my experience seems to occur in the closing minutes (often seconds)particulalry for very cheap, very expensive or sought after items.