Installed ftp://ftp.squeak.org/3.9Beta/Squeak3.9b-7029.zip running on VM Squeak 3.8.12beta4U.app on Mac G5 with OS X 10.4.6.

On first trying to open a transcript, I get "Which ToolSet would you prefer?" #PlusToolSet or #StandardToolSet, I select #PlusToolSet, then open a Transcript ok. Then attempt to open a File List and get a message window saying
UndefinedObject(Object)>>doesNotUnderstand: #leftOffset
PluggableSystemWindow(SystemWindow)>>addMorph:fullFrame:
PluggableSystemWindow>>addPaneMorph:
MorphicToolBuilder>>add:to:
MorphicToolBuilder>>buildPluggableButton:
MorphicToolBuilder>>buildPluggableActionButton:
PluggableActionButtonSpec>>buildWith:
MorphicToolBuilder(ToolBuilder)>>build:
[] in FileListPlus>>getButtonRow {[:service |  buttonSpec := builder pluggableActionButtonSpec new.  buttonSpe...]}
Array(SequenceableCollection)>>collect:

Meanwhile the Transcript window displays "Warning: pane preDebugMessageString not found."
This does not occur if #StandardToolSet is the choice on startup.
--------------------------------------------------------------------------------
Then with #StandardToolSet selected on startup:

Try Open SqueakMap Package Browser
	Get notifier saying SqueakMap server version is newer (2.2) than client (2.0), upgrade to new version Yes/No.
Select Yes, then after some time "Upgrading SqueakMap", get a primitive failed error. This is with no sm or package-cache folders present on Squeak startup.

Contents of SqueakDebug.log after starting the Debugger at this point:

Error: a primitive has failed
7 May 2006 7:23:36 pm

VM: Mac OS - a SmalltalkImage
Image: Squeak3.9alpha [latest update: #7028]

SecurityManager state:
Restricted: false
FileAccess: true
SocketAccess: true
Working Dir /Squeak3.9b-7029 Folder
Trusted Dir /Squeak3.9b-7029 Folder
Untrusted Dir /Users/kbrown/Library/Preferences/Squeak/Internet/My Squeak

ByteString class(Object)>>error:
	Receiver: ByteString
	Arguments and temporary variables:
		aString:	'a primitive has failed'
	Receiver's instance variables:
		superclass:	String
		methodDict:	a MethodDictionary(#asByteArray->a CompiledMethod (2960) #asOctetSt...etc...
		format:	23554
		traitComposition:	{}
		localSelectors:	nil
		instanceVariables:	nil
		organization:	('accessing' at: at:put: byteAt: byteAt:put: byteSize replaceFrom...etc...
		subclasses:	nil
		name:	#ByteString
		classPool:	nil
		sharedPools:	nil
		environment:	a SystemDictionary(lots of globals)
		category:	#'Collections-Strings'

ByteString class(Object)>>primitiveFailed
	Receiver: ByteString
	Arguments and temporary variables:

	Receiver's instance variables:
		superclass:	String
		methodDict:	a MethodDictionary(#asByteArray->a CompiledMethod (2960) #asOctetSt...etc...
		format:	23554
		traitComposition:	{}
		localSelectors:	nil
		instanceVariables:	nil
		organization:	('accessing' at: at:put: byteAt: byteAt:put: byteSize replaceFrom...etc...
		subclasses:	nil
		name:	#ByteString
		classPool:	nil
		sharedPools:	nil
		environment:	a SystemDictionary(lots of globals)
		category:	#'Collections-Strings'

ByteString class(Behavior)>>basicNew:
	Receiver: ByteString
	Arguments and temporary variables:
		sizeRequested:	-1
	Receiver's instance variables:
		superclass:	String
		methodDict:	a MethodDictionary(#asByteArray->a CompiledMethod (2960) #asOctetSt...etc...
		format:	23554
		traitComposition:	{}
		localSelectors:	nil
		instanceVariables:	nil
		organization:	('accessing' at: at:put: byteAt: byteAt:put: byteSize replaceFrom...etc...
		subclasses:	nil
		name:	#ByteString
		classPool:	nil
		sharedPools:	nil
		environment:	a SystemDictionary(lots of globals)
		category:	#'Collections-Strings'

ByteString class(String class)>>new:
	Receiver: ByteString
	Arguments and temporary variables:
		sizeRequested:	-1
	Receiver's instance variables:
		superclass:	String
		methodDict:	a MethodDictionary(#asByteArray->a CompiledMethod (2960) #asOctetSt...etc...
		format:	23554
		traitComposition:	{}
		localSelectors:	nil
		instanceVariables:	nil
		organization:	('accessing' at: at:put: byteAt: byteAt:put: byteSize replaceFrom...etc...
		subclasses:	nil
		name:	#ByteString
		classPool:	nil
		sharedPools:	nil
		environment:	a SystemDictionary(lots of globals)
		category:	#'Collections-Strings'


--- The full stack ---
ByteString class(Object)>>error:
ByteString class(Object)>>primitiveFailed
ByteString class(Behavior)>>basicNew:
ByteString class(String class)>>new:
 - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
ByteString(SequenceableCollection)>>copyFrom:to:
ByteString(SequenceableCollection)>>first:
SMSqueakMap>>saveCheckpoint:
[] in SMSqueakMap>>loadFullFrom: {[self saveCheckpoint: zipped]}
Time class>>millisecondsToRun:
SMSqueakMap>>loadFullFrom:
SMSqueakMap>>loadUpdatesFull:
SMSqueakMap>>loadFull
SMSqueakMap>>loadUpdates
[] in UndefinedObject>>DoIt {[(Smalltalk hasClassNamed: #SMLoader)   ifTrue: [(Smalltalk at: #SMLoader) a...]}
BlockContext>>ensure:
CursorWithMask(Cursor)>>showWhile:
UndefinedObject>>DoIt
Compiler>>evaluate:in:to:notifying:ifFail:logged:
Compiler class>>evaluate:for:notifying:logged:
Compiler class>>evaluate:for:logged:
Compiler class>>evaluate:logged:
[] in ReadStream(PositionableStream)>>fileInAnnouncing: {[val := (self peekFor: $!)     ifTrue: [(Compiler evaluate: self nextChunk l...]}
BlockContext>>on:do:
[] in ReadStream(PositionableStream)>>fileInAnnouncing: {[:bar |  [self atEnd]   whileFalse: [bar value: self position.    self skipS...]}
[] in ProgressInitiationException>>defaultMorphicAction {[result := workBlock value: progress]}
BlockContext>>ensure:
ProgressInitiationException>>defaultMorphicAction
ProgressInitiationException>>defaultAction
UndefinedObject>>handleSignal:
MethodContext(ContextPart)>>handleSignal:
MethodContext(ContextPart)>>handleSignal:
ProgressInitiationException(Exception)>>signal
...etc...

Note that the log says latest update is #7028, not #7029.
Hope this helps.
   Ken Brown