Arduino 1.5.6-r2 Memory Error / Compiling Error

I have just ordered a Yun and I have been using the new IDE 1.5.6-r2 and having issues with compiling errors...
The sketch is for my Aquarium Computer Project and it compiles and runs just fine with Arduino IDE 1.0.5-r2. Board is Leonardo and Windows 7. This is the compile message from 1.0.5-r2 IDE:

Binary sketch size: 28,468 bytes (of a 28,672 byte maximum)

However the same sketch is Arduino IDE 1.5.6-r2 and Leonardo selected as the board I get the below error:
Build options changed, rebuilding all

Sketch uses 28,676 bytes (100%) of program storage space. Maximum is 28,672 bytes.
Global variables use 4,140 bytes (161%) of dynamic memory, leaving -1,580 bytes for local variables. Maximum is 2,560 bytes.
processing.app.debug.RunnerException: Sketch too big; see http://www.arduino.cc/en/Guide/Troubleshooting#size for tips on reducing it.
at processing.app.Sketch.size(Sketch.java:1676)
at processing.app.Sketch.build(Sketch.java:1590)
at processing.app.Sketch.build(Sketch.java:1509)
at processing.app.Editor$DefaultRunHandler.run(Editor.java:1915)
at java.lang.Thread.run(Unknown Source)

I can reduce the sketch size to get that below the 28,672 but Dynamic Memory?
Any Thoughts....Carl.

just use the 1.0.5 environment, if the sketch works it works,
no need to have the latest greatest .... beta

It may compile with IDE v1.0.5, but does it run without crashing? This message in v1.5.6 would indicate it will crash.

Global variables use 4,140 bytes (161%) of dynamic memory, leaving -1,580 bytes for local variables. Maximum is 2,560 bytes.