Safari 6.1.1 stuttering while playing Flash

Question

Does anyone know why has Safari started to stutter while playing Flash video? No matter the size of the content provider (in my case Lynda), it stops for a fraction of a second every 3 seconds. It is QUITE annoying! And, I'm sure it is Safari, I've played those videos an hour before I updated to Safari 6.1.1 and now it is Flash mayhem! I'm tempted to recover (the whole system, thank you very much, Apple) from Time Machine so I do away with this MAJOR annoyance! Any suggestions?

Answer 1

Dominic, thank you for a boiler-plate instructions, I did many, if not all, of those before posting.
However, the story deepens, it sems that the culprit is one of the system updates, since this happened to me on a different machine, too. At least, culprit would be the part of one of the updates that may have written to/changed permissions of the ScriptingAdditions folder. Or, the sandbox settings may have been corrupted, who knows, I don't.
Here's the detailed report that was being generated in Console log ***repetitively***:
PluginProcess(25190) deny file-read-data /Users/[user]/Library/ScriptingAdditions
Process:         PluginProcess [25190]
Path:            /System/Library/StagedFrameworks/Safari/WebKit2.framework/PluginProcess.app/Con tents/MacOS/PluginProcess
Load Address:    0x109d5f000
Identifier:      PluginProcess
Version:         ??? (???)
Code Type:       X86-64 (Native)
Parent Process:  Safari [24555]
Date/Time:       2014-01-23 17:40:14.783 -0600
OS Version:      Mac OS X 10.7.5 (11G63)
Report Version:  7
Backtrace:
0   libsystem_kernel.dylib                  0x00007fff8c1c5afa __open_nocancel + 10
1   libsystem_c.dylib                       0x00007fff8c05d033 __opendir2$INODE64 + 51
2   CarbonCore                              0x00007fff8dc71d71 FSMount::getIndexedDirectoryItem(unsigned int, unsigned int, unsigned int, char*, unsigned char*) + 283
3   CarbonCore                              0x00007fff8dc25f9e PBGetCatalogInfoBulkSync + 941
4   CarbonCore                              0x00007fff8dc25bd4 FSGetCatalogInfoBulk + 66
5   OpenScripting                           0x00007fff8e0933f4 _ZL13IterateFolderPK5FSRefP6AEDescsbb + 209
6   OpenScripting                           0x00007fff8e093cc6 _ZL13LoadAdditionsP6AEDesc + 502
7   OpenScripting                           0x00007fff8e0943a0 HandleGDUT(AEDesc const*, AEDesc*, void*) + 260
8   AE                                      0x00007fff911a5c25 aeDispatchAppleEvent(AEDesc const*, AEDesc*, unsigned int, unsigned char*) + 200
9   AE                                      0x00007fff911a5b03 _ZL25dispatchEventAndSendReplyPK6AEDescPS_ + 38
10  AE                                      0x00007fff911a59f7 aeProcessAppleEvent + 250
11  HIToolbox                               0x00007fff8bb52b69 AEProcessAppleEvent + 102
12  AppKit                                  0x00007fff894929c5 _DPSNextEvent + 1247
13  AppKit                                  0x00007fff8949207d -[NSApplication nextEventMatchingMask:untilDate:inMode:dequeue:] + 135
14  AppKit                                  0x00007fff8948e9b9 -[NSApplication run] + 470
15  WebKit2                                 0x0000000109f8e14f int WebKit::ChildProcessMain<WebKit::PluginProcess, WebKit::PluginProcessMainDelegate>(int, char**) + 645
16  PluginProcess                           0x0000000109d60b7f
17  PluginProcess                           0x0000000109d60a78
Binary Images:
       0x109d5f000 -        0x109d61fff  com.apple.WebKit.PluginProcess (7537 - 7537.73.11) <94FB3F7B-A0D6-34F0-957C-FE7DF08C9FE3> /System/Library/StagedFrameworks/Safari/WebKit2.framework/PluginProcess.app/Con tents/MacOS/PluginProcess
       0x109f00000 -        0x10a168fff  com.apple.WebKit2 (7537 - 7537.73.11) <ADBE17E6-F45E-340B-9172-09C9E25389E9> /System/Library/StagedFrameworks/Safari/WebKit2.framework/WebKit2
    0x7fff8948a000 -     0x7fff8a090fff  com.apple.AppKit (6.7.5 - 1138.51) <44417D02-6123-3FC3-A119-CE51BB4C3006> /System/Library/Frameworks/AppKit.framework/Versions/C/AppKit
    0x7fff8bb42000 -     0x7fff8be6efff  com.apple.HIToolbox (1.9 - ???) <CCB32DEA-D0CA-35D1-8019-E599C8007AB6> /System/Library/Frameworks/Carbon.framework/Versions/A/Frameworks/HIToolbox.fra mework/Versions/A/HIToolbox
    0x7fff8c002000 -     0x7fff8c0dffef  libsystem_c.dylib (763.13.0 - compatibility 1.0.0) <41B43515-2806-3FBC-ACF1-A16F35B7E290> /usr/lib/system/libsystem_c.dylib
    0x7fff8c1af000 -     0x7fff8c1cffff  libsystem_kernel.dylib (1699.32.7 - compatibility 1.0.0) <66C9F9BD-C7B3-30D4-B1A0-03C8A6392351> /usr/lib/system/libsystem_kernel.dylib
    0x7fff8dc08000 -     0x7fff8df24fff  com.apple.CoreServices.CarbonCore (960.25 - 960.25) <4FC1AB30-022C-3C67-AC46-FDCBFCB7EEDE> /System/Library/Frameworks/CoreServices.framework/Versions/A/Frameworks/CarbonC ore.framework/Versions/A/CarbonCore
    0x7fff8e081000 -     0x7fff8e09eff7  com.apple.openscripting (1.3.3 - ???) <F5E34F54-CE85-334B-8F25-53581D43960C> /System/Library/Frameworks/Carbon.framework/Versions/A/Frameworks/OpenScripting .framework/Versions/A/OpenScripting
    0x7fff911a2000 -     0x7fff911e1fff  com.apple.AE (527.7 - 527.7) <B82F7ABC-AC8B-3507-B029-969DD5CA813D> /System/Library/Frameworks/CoreServices.framework/Versions/A/Frameworks/AE.fram ework/Versions/A/AE
(I blanked out my user name.)