If my interpretation is correct, you think randomly generated decks for each shuffle will produce a different result than a hand shuffled deck. This has been proven to be false many years ago.
Software was developed that allowed you to created your own shuffles based on casino shuffles. No matter how sloppy the shuffles got, there was no detectable pattern in the distribution of the cards in the deck based on the last deck.
The reason you may have losses at single deck blackjack is not because the software you use to practice isn't arranging the cards like they do in a casino. It is because you don't play it very often.
Taking %20 of your shoe winnings and not re buying is problematic for single deck. Single deck has the highest EV, but also the highest variance due to the huge swings in advantage.
Using this calculator http://www.bjstats.com/bjre.asp
and inputting the most ideal scenario, I'm coming up with at least 2508 hands of blackjack before you reach the long run. That is probably 25 hours of play if you are moving at a good clip.
Keep in mind, this is using Advanced Omega II with full indices and an ace side count. You are spreading 1-20 and there is good penetration. Rules are S17, DAS, late surrender. You will never, ever, EVER, find a game this good....unless it is either a counter trap or soon being removed by the casino (due to being crushed by counters)
Let's try a more realistic scenario. Since you said PERFECT counting, I'm going to stick with AOII w/ Ace side count and full indices. However, the pen is only fair, you are spreading 1-4, and the rules are H17, no DAS, no surrender.
Now it takes you 9333 hands to reach the long run. 93 hours and 20 minutes of straight blackjack if you can manage 100 hands an hour.
One last tweak, lets change the count to High-Low with I18 and Fab 4. Now it takes you 14412 hands to reach the long run. That is 144+ hours of blackjack before you are close to your expected value.
Let's make your average bet $25 and you EV is 1.15% (very good considering most situations get .5% at best, this is why wonging is so popular in today's game)
You will wager a total of $360,300 and will have won around $4143.45.
That is about $28 dollars an hour, not bad pay, but it isn't like you work full time.
One last thing regarding your complaints of heat. How many single deck games are there in that casino? If there are only a few compared to quite a few shoe games, then they are most likely counter traps. Playing those gets you heat, while sticking to the shoe games will get you far less.