On the leaderboard it shows the cores left and towers built for the current game you did, not the one you got the high score with. So if you just let all the cores go and build 0 towers, it will look like

0 0 oldscore



Checkpoints are warping as with the aliens.

For example

When the checkpoint hits it looks like this
= is aliens
| is the radar bar

| ...................................... = = = =

when you reload the checkpoint it looks like this

| = = = =

This not only loses you a lot of interest, it also makes aliens and flyers come out instantly after the checkpoints.



For example the last checkpoint on last stand.

The first time you hit the checkpoint you have time to build the missile towers also check the score when it hits | = now go back to the checkpoint and you will see the flyers come out straight away, and you have lost resources at | =.



Also i think using exit and continue also does it as my exact same setup had lost resources, and i had replicated it a few times before and it was the same each go.