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Bug reports without an attached log file are usually useless.
Here is WinSCP3.ini, which 100% causes strange effects:
[Configuration\Interface]
RandomSeedFile=C:%5CDocuments%20and%20Settings%5CGringo%5Cwinscp.RND
ConfirmOverwriting=1
CopyParamDialogExpanded=1
ErrorDialogExpanded=1
ContinueOnError=0
SynchronizeParams=3
QueueTransfersLimit=1
QueueAutoPopup=1
PuttySession=WinSCP%20temporary%20session
PuttyPath=D:%5CApps%5CPuTTY%200.54%5CPUTTY.EXE
IgnoreCancelBeforeFinish=30.12.1899 0:00:03
Interface=1
ShowAdvancedLoginOptions=1
CopyOnDoubleClick=0
CopyOnDoubleClickConfirmation=0
DDAllowMove=0
DDAllowMoveInit=0
DDTransferConfirmation=1
DDTemporaryDirectory=
DDWarnLackOfTempSpace=1
DDWarnLackOfTempSpaceRatio=1,1
DeleteToRecycleBin=1
DimmHiddenFiles=1
SelectDirectories=0
SelectMask=%2A.%2A
ShowHiddenFiles=1
ShowInaccesibleDirectories=1
ConfirmDeleting=1
ConfirmClosingSession=1
ConfirmExitOnCompletion=1
AutoStartSession=
UseLocationProfiles=0
ForceDeleteTempFolder=1
LocaleSafe=1033
DDExtEnabled=1
DDExtTimeout=1000
DDExtCopySlipTimeout=100
DefaultDirIsHome=1
[Configuration\Interface\CopyParam]
AddXToDirectories=1
Masks=%2A.%2Ahtml;%20%2A.htm;%20%2A.txt;%20%2A.php%2A;%20%2A.cgi;%20%2A.c;%20%2A.cpp;%20%2A.h;%20%2A.pas;%20%2A.bas;%20%2A.tex;%20%2A.pl;%20.htaccess;%20%2A.xtml;%20%2A.css;%20%2A.cfg;%20%2A.ini;%20%2A.sh;%20%2A.xml
FileNameCase=0
PreserveReadOnly=1
PreserveTime=1
PreserveRights=1
Text=rw-r-----
TransferMode=0
ResumeSupport=1
ResumeThreshold=102400
ReplaceInvalidChars=1
LocalInvalidChars=/%5C:%2A%3F"<>|
CalculateSize=1
[Configuration\Logging]
Logging=0
LogFileName=
LogFileAppend=1
LogWindowLines=100
LogView=0
LogWindowOnStartup=1
LogWindowParams=-1;-1;500;400
[Configuration\Interface\Editor]
Editor=0
ExternalEditor=notepad.exe%20!.!
ExternalEditorText=1
FontName=Courier%20New
FontHeight=-12
FontStyle=0
FontCharset=1
WordWrap=0
FindText=
ReplaceText=
FindMatchCase=0
FindWholeWord=0
[Configuration\Interface\QueueView]
Height=110
Layout=70,170,170,80,80
Show=0
ToolBar=1
[Configuration\Interface\Explorer]
CoolBarLayout=5,1,0,140,6;3,0,0,127,5;4,1,0,490,4;6,0,0,196,3;2,1,1,634,2;1,1,0,638,1;0,1,1,634,0
DirViewParams=0;1;0|150,1;70,1;101,1;79,1;62,1;55,1;20,0|0;1;2;3;4;5;6
LastLocalTargetDirectory=C:%5CDocuments%20and%20Settings%5CGringo%5CDesktop%5C
StatusBar=1
WindowParams=170;49;818;496;0
ViewStyle=2
ShowFullAddress=1
[Configuration\Interface\Commander]
CoolBarLayout=5,0,0,219,6;1,1,0,522,5;4,0,0,227,4;3,1,0,137,3;6,1,0,145,2;2,1,1,104,1;0,1,1,920,0
CurrentPanel=1
LocalPanelWidth=0,5
StatusBar=1
CommandLine=0
ToolBar=1
WindowParams=66;94;1000;708;0
ExplorerStyleSelection=0
PreserveLocalDirectory=0
CompareByTime=1
CompareBySize=0
SynchronizeBrowsing=1
[Configuration\Interface\Commander\LocalPanel]
CoolBarLayout=2,1,0,137,2;1,1,0,86,1;0,1,1,223,0
DirViewParams=0;1;0|150,1;70,1;101,1;79,1;62,1;55,0|0;1;2;3;4;5
StatusBar=1
[Configuration\Interface\Commander\RemotePanel]
CoolBarLayout=2,1,0,137,2;1,1,0,86,1;0,1,1,224,0
DirViewParams=0;1;0|150,1;70,1;101,1;79,1;62,1;55,0;20,0|0;1;2;3;4;5;6
StatusBar=1
[Configuration\CustomCommands]
&Execute="!"
&Touch=touch%20"!"
Ta&r/GZip=tar%20-cz%20%20-f%20"!%3F&Archive%20Name:%3Farchive.tgz!"%20"!"
&UnTar/GZip=tar%20-xz%20--directory="!%3F&Extract%20to%20directory:%3F.!"%20-f%20"!"
[Configuration\CustomCommandsParams]
&Execute=0
&Touch=3
Ta&r/GZip=1
&UnTar/GZip=0