UPDATE2: You were close. You want to set the decimal places to 2 values before you add commas. See also Number::Format. This works for me:

      $format_main_balance = format_value(sprintf("%.2f",$main_balance
+));
[download]

UPDATE1: I just read-read your question, and I now see the decimal dropped for 900,000.

OLD... IGNORE: When I run your code, it seems to keep decimals. Here is the output I get:

DATE        DESCRIPTION                               DEBIT       CRED
+IT      BALANCE   
======================================================================
+==================
2017-05-01  starting balance to track character cou~              900,
+000.00     900,000
2017-05-01  phone bill dsfsdfsfdsfsfsfsdfsfsfsfsfdf~  300,000.00      
+           600,000
2017-05-03  Water                                     100,000.34      
+        499,999.66
2017-05-05  Electric Bill                                 900.21      
+        499,099.45
2017-06-03  debit 45678901dfsf2345678901234567890dd~       30.32      
+        499,069.13
2017-06-03  12345678901234567890123456789034                          
+ 30.98  499,100.11
2017-06-03  credit 89012345678901234567890345678901~                  
+ 30.98  499,131.09
2017-06-03  credit dfdfd012345678901234567890345678~                  
+ 30.98  499,162.07
2017-06-08  Food                                           23.00      
+        499,139.07
2017-06-12  Cash                                           20.00      
+        499,119.07
[download]

Do you get a different output? If so, post exactly what you get. I'm using Perl version 5.16.3.

Basic debugging checklist