[Galaxy S II Android Development] Dr01nE:
May not really help but.. here's my findings after using WinMerge:

Stock vs. Modified file (services.rar):

ActivityManagerService.smali

- Attached code was removed from Modded Services

:cond_a
move/from16 v0, v23

and-int/lit16 v2, v0, 0x80

if-eqz v2, :cond_4

.line 14274
move-object/from16 v0, v28

iget-object v2, v0, Landroid/content/res/Configuration;->centerBarRect:Landroid/graphics/Rect;

if-eqz v2, :cond_4

.line 14275
invoke-static {}, Landroid/sec/multiwindow/impl/MultiWindowManager;->getSplitDirection()I

move-result v2

move-object/from16 v0, v28

iget v3, v0, Landroid/content/res/Configuration;->orientation:I

if-eq v2, v3, :cond_4

.line 14276
new-instance v29, Landroid/graphics/Rect;

move-object/from16 v0, v28

iget-object v2, v0, Landroid/content/res/Configuration;->centerBarRect:Landroid/graphics/Rect;

iget v2, v2, Landroid/graphics/Rect;->top:I

move-object/from16 v0, v28

iget-object v3, v0, Landroid/content/res/Configuration;->centerBarRect:Landroid/graphics/Rect;

iget v3, v3, Landroid/graphics/Rect;->left:I

move-object/from16 v0, v28

iget-object v4, v0, Landroid/content/res/Configuration;->centerBarRect:Landroid/graphics/Rect;

iget v4, v4, Landroid/graphics/Rect;->bottom:I

move-object/from16 v0, v28

iget-object v6, v0, Landroid/content/res/Configuration;->centerBarRect:Landroid/graphics/Rect;

iget v6, v6, Landroid/graphics/Rect;->right:I

move-object/from16 v0, v29

invoke-direct {v0, v2, v3, v4, v6}, Landroid/graphics/Rect;-><init>(IIII)V

.line 14278
.local v29, rotatedCenterBarRect:Landroid/graphics/Rect;
move-object/from16 v0, p0

iget-object v2, v0, Lcom/android/server/am/ActivityManagerService;->mWindowManager:Lcom/android/server/wm/WindowManagerService;

move-object/from16 v0, v29

invoke-virtual {v2, v0}, Lcom/android/server/wm/WindowManagerService;->updateCenterBarRect(Landroid/graphics/Rect;)V

.line 14279
move-object/from16 v0, v28

iget v2, v0, Landroid/content/res/Configuration;->orientation:I

move-object/from16 v0, v29

invoke-static {v2, v0}, Landroid/sec/multiwindow/impl/MultiWindowManager;->setSplitRect(ILandroid/graphics/Rect;)V

.line 14280
move-object/from16 v0, v28

iget-object v2, v0, Landroid/content/res/Configuration;->centerBarRect:Landroid/graphics/Rect;

move-object/from16 v0, v29

invoke-virtual {v2, v0}, Landroid/graphics/Rect;->set(Landroid/graphics/Rect;)V

goto/16 :goto_2

.line 14330
.end local v29 #rotatedCenterBarRect:Landroid/graphics/Rect;

ActivityRecord.smali

- Attached code was deleted from modified services.jar

move-object/from16 v0, p7

iget v11, v0, Landroid/content/pm/ActivityInfo;->screenOrientation:I

if-eqz v11, :cond_18

move-object/from16 v0, p7

iget v11, v0, Landroid/content/pm/ActivityInfo;->screenOrientation:I

const/4 v12, 0x1

if-ne v11, v12, :cond_19

.line 609
:cond_18
const/high16 v11, 0x100

iput v11, p0, Lcom/android/server/am/ActivityRecord;->currentWindowMode:I

.line 612
:cond_19

const/high16 v8, 0x20

and-int/2addr v7, v8

if-eqz v7, :cond_16

.line 288
const-string v7, "resize, "

invoke-virtual {p1, v7}, Ljava/io/PrintWriter;->print(Ljava/lang/String;)V

.line 291
:cond_16
iget v7, p0, Lcom/android/server/am/ActivityRecord;->currentWindowMode:I

invoke-static {v7}, Landroid/view/WindowManagerPolicy$WindowModeHelper;->option(I)I

move-result v7

and-int/lit16 v7, v7, 0x2000

if-eqz v7, :cond_17

.line 293
const-string v7, "forcetitlebar, "

invoke-virtual {p1, v7}, Ljava/io/PrintWriter;->print(Ljava/lang/String;)V

.line 296
:cond_17
iget v7, p0, Lcom/android/server/am/ActivityRecord;->currentWindowMode:I

invoke-static {v7}, Landroid/view/WindowManagerPolicy$WindowModeHelper;->option(I)I

move-result v7

[COLOR="Red"]nop[/COLOR] [COLOR="Green"]#Deleted on Modified[/COLOR]

:sswitch_data_0
.sparse-switch
0x1000000 -> :sswitch_0
0x2000000 -> :sswitch_1
.end sparse-switch
.end method

AppErrorDialog.smali

From:

#the value of this static final field might be set in the static constructor
.field static final DISMISS_TIMEOUT:J = 0x0L

To:

.field static final DISMISS_TIMEOUT:J = 0x493e0L

From:

sget-wide v6, Lcom/android/server/am/AppErrorDialog;->DISMISS_TIMEOUT:J

To:

const-wide/32 v6, 0x493e0

- This method was deleted on modded services.jar

.method static constructor <clinit>()V
.locals 3

.prologue
const/4 v2, 0x1

.line 53
invoke-static {}, Landroid/os/Debug;->isProductShip()I

move-result v0

if-ne v0, v2, :cond_0

invoke-static {}, Lcom/sec/android/app/CscFeature;->getInstance()Lcom/sec/android/app/CscFeature;

move-result-object v0

const-string v1, "CscFeature_Framework_DisableForceClosePopup"

invoke-virtual {v0, v1}, Lcom/sec/android/app/CscFeature;->getEnableStatus(Ljava/lang/String;)Z

move-result v0

if-ne v0, v2, :cond_0

.line 54
const-wide/16 v0, 0x0

sput-wide v0, Lcom/android/server/am/AppErrorDialog;->DISMISS_TIMEOUT:J

.line 58
:goto_0
return-void

.line 56
:cond_0
const-wide/32 v0, 0x493e0

sput-wide v0, Lcom/android/server/am/AppErrorDialog;->DISMISS_TIMEOUT:J

goto :goto_0
.end method

BaseErrorDialog.smali, ActivityManagerService$2.smali, & LaunchWarningWindow.smali

- Public ID Mismatch (1 instance on each file)

MultiWindowManagerService.smali & ActivityStack.smali

- Multiple modifications