Particle order. Subframe relies on this nasty/awesome thing (:P) called particle order. When saves are reopened, particles are ordered left to right, top to bottom. This determines what order each particle will be executed in, and subframe heavily relies on this. Increasingly, in this order, the particles are assigned particle IDs. The lower the ID, the earlier it is executed. 

(For solid spark, the order should be POWERED MATERIAL (e.g. ARAY) -> CONDUCTOR (METL) -> CONV -> BTRY 

Oh, and before you reopen the save, particle order is determined by the order in which you draw stuff.

To answer your question, you must predict the order of execution for each particle you place. It isn't too hard. Just remember: Left-right, Top-Bottom.

In case you haven't seen it already, LBPHacker made an awesome save on it.

When you "local save" a simulation, TPT "serialises" the simulation data before storing it. What this means is that TPT arranges all particles in order from left-to-right, top-to-bottom, so if your particles weren't arranged that way before, the particle order would change and the creation would break.

The problem is that when you draw particles, TPT does not arrange them in order immediately, because that would slow things down. This means that after you draw a circuit, the particles are almost never in the left-to-right, top-to-bottom order, and the circuit would almost certainly break upon saving and reloading.

The way to get around this is to always rearrange the particles after you've drawn a circuit, before testing to see if it works. You can do this in a number of ways:

1. Actually saving and reloading (rather tedious)
2. Using a Lua script (you might need to change the key combination, though, if you're on Ubuntu)
3. Using a mod that does it automatically for you (shameless self-promotion)

This also means that you have to design subframe circuits with particle order in mind. There is no trial-and-error involved. Ensure that, if you arrange the particles in order from left-to-right, top-to-bottom, you have ARAY, CONV, BTRY in that order.

And no, there isn't a "local save" that preserves messed-up particle order. Besides, you wouldn't want that because then you won't be able to share your circuit with others (uploading to TPT's server reorders particles too).

EDIT: Oops, ninja'ed.

@mark2222 :))))

@CrustyBunz I'd never get mad at someone for not understanding something (unless it is myself.)