I solved this problem on archlinux by setting the line StartupMinimized=0 to StartupMinimized=1 I am attaching my amule.conf and if interested in someone, just change your_name with the name of your home (are 3 lines to change).
[eMule]
AppVersion=2.2.6
Nick=http://www.aMule.org
NewVersionCheck=1
StartupMinimized=1
ConfirmExit=1
EnableTrayIcon=0
MinToTray=0
ToolTipDelay=1
VideoPlayer=totem
VideoPreviewBackupped=1
MaxDownload=400
MaxUpload=10
SlotAllocation=2
Port=4662
UDPPort=4672
UDPDisable=0
Address=
MaxSourcesPerFile=300
MaxConnections=500
ConnectToED2K=1
ConnectToKad=1
UPnPEnabled=0
UPnPTCPPort=50000
Autoconnect=1
Reconnect=1
ShowOverhead=0
RemoveDeadServer=1
DeadServerRetry=3
Serverlist=0
AddServerListFromServer=0
AddServerListFromClient=0
Scoresystem=1
SmartIdCheck=1
SafeServerConnect=0
AutoConnectStaticOnly=0
ManualHighPrio=0
ICH=1
AICHTrust=0
AddNewFilesPaused=0
DAPPref=1
PreviewPrio=0
UAPPref=1
FullChunkTransfers=1
StartNextFile=0
StartNextFileSameCat=0
CheckDiskspace=1
MinFreeDiskSpace=1
AllocateFullFile=0
IncomingDir=/home/your_name/.aMule/Incoming
TempDir=/home/your_name/.aMule/Temp
ShareHiddenFiles=0
StatGraphsInterval=3
StatsAverageMinutes=5
VariousStatisticsMaxValue=100
statsInterval=30
DownloadCapacity=300
UploadCapacity=100
MaxConnectionsPerFiveSeconds=20
FileBufferSizePref=16
QueueSizePref=50
ServerKeepAliveTimeout=0
3DDepth=5
AutoSortDownloads=0
ShowInfoOnCatTabs=1
ShowRatesOnTitle=0
VerticalToolbar=0
ShowPartFileNumber=0
SeeShare=2
IPFilterURL=
IPFilterAutoLoad=1
FilterLevel=127
FilterLanIPs=1
ParanoidFiltering=1
IPFilterSystem=0
OnlineSignature=0
OnlineSignatureUpdate=5
OSDirectory= /home/your_name/.aMule/
FilterMessages=1
FilterAllMessages=0
MessagesFromFriendsOnly=0
MessageFromValidSourcesOnly=1
FilterWordMessages=0
MessageFilter=
FilterComments=0
CommentFilter=
Language=
SplitterbarPosition=75
YourHostname=
DateTimeFormat=%A, %x, %X
AllcatType=0
ShowAllNotCats=0
SmartIdState=1
DropSlowSources=0
KadNodesUrl=http://emule-inside.net/nodes.dat
Ed2kServersUrl=http://gruk.org/server.met.gz
StatColor0=4194304
StatColor1=16761024
StatColor2=8454016
StatColor3=53760
StatColor4=32768
StatColor5=8421631
StatColor6=200
StatColor7=140
StatColor8=16750230
StatColor9=12583104
StatColor10=8454143
StatColor11=0
StatColor12=8454016
StatColor13=53760
StatColor14=32768
TableOrderingServer=0 0,
TableWidthsServer=150,140,25,150,25,40,45,60,40,40,80
TableOrderingDownload=0 0,
TableWidthsDownload=260,60,65,65,65,170,50,55,70,110,220,220
TableOrderingUploads=0 0,
TableWidthsUploads=150,275,100,60,65,60,60,110,100,100,100
TableOrderingShared=0 0,
TableWidthsShared=250,100,50,70,220,100,100,120,100,120,120,220
[Browser]
DefaultBrowser=3
CustomBrowserString=
OpenPageInTab=1
[ExternalConnect]
UseSrcSeeds=0
ShowPercent=1
ShowProgressBar=1
AcceptExternalConnections=0
ECPassword=
ECAddress=
ECPort=4712
UPnPECEnabled=0
IpFilterClients=1
IpFilterServers=1
UseSecIdent=1
[Statistics]
MaxClientVersions=0
TotalDownloadedBytes=0
TotalUploadedBytes=5394
[SkinGUIOptions]
UseSkinFiles=0
Skin=System:gnome.zip
[Razor_Preferences]
FastED2KLinksHandler=1
SRV_SPLITTER_POS=248
MAIN_X_POS=319
MAIN_Y_POS=116
MAIN_X_SIZE=800
MAIN_Y_SIZE=600
Maximized=0
[WebServer]
Enabled=0
Port=4711
UPnPWebServerEnabled=0
WebUPnPTCPPort=50001
PageRefreshTime=120
UseGzip=1
UseLowRightsUser=0
Password=
PasswordLow=
Template=litoral
[Obfuscation]
IsClientCryptLayerSupported=1
IsCryptLayerRequested=1
IsClientCryptLayerRequired=0
CryptoPaddingLenght=254
CryptoKadUDPKey=-1048519488
[Proxy]
ProxyEnableProxy=0
ProxyType=0
ProxyName=
ProxyPort=1080
ProxyEnablePassword=0
ProxyUser=
ProxyPassword=
[UserEvents]
[UserEvents/DownloadCompleted]
CoreEnabled=0
CoreCommand=
GUIEnabled=0
GUICommand=
[UserEvents/NewChatSession]
CoreEnabled=0
CoreCommand=
GUIEnabled=0
GUICommand=
[UserEvents/OutOfDiskSpace]
CoreEnabled=0
CoreCommand=
GUIEnabled=0
GUICommand=
[UserEvents/ErrorOnCompletion]
CoreEnabled=0
CoreCommand=
GUIEnabled=0
GUICommand=
[GUI]
[GUI/TransferWnd]
Splitter=445
ShowClientList=1
It works with version 2.2.6 and I hope it can help someone.
Have a nice day.