Creating Formulas but not responding as expected.. Due to format of cell?

I have a large moderately complex workbook for forecasting / projecting a financial situation for next 30 years.
It references data on multiple sheets. I'm using Accounting format, but I have removed / shifted the decimal places so it shows Custom for the format.
It has been working fine, but yesterday when I attempted some changes, all of a sudden when I create a formula, even something as simple as =H36 or as simple IF statement, the cell remains empty or shows 0!
I just tried something in some unused cells, where I did a simple =E31, which contains the value 12%. Three of the four cells show 12% the other $  0. The three that show 12% were probably General to start, but now show percentage. The one that didn't show 12%, was Custom, from me using it previously to test thigs. 
I then formatted a blank cell Accounting and shifted decimals (sand it reacts the same way, and show $  0, not 12%.

What is going on? LOL

E31 is manually entered 12%

I entered =E31 in each of these cells below. (It won't let me use a table here...) They started as General. The one that doesn't show 12% was preformatted Accounting but with decimals shifted, so it shows Custom. The last one I formatted as Accounting without removing / shifting the decimals and it pulled in the 12%...  I'm lost. What's gone whacky with the Custom format after shifting the decimals? It has been working fine. 

Thanks

12%

12%

$  0

12%

12%

12%