> It's not a bug nor a known problem. You didn't install/configure ClamAV 
> properly.

I did install it properly as there isn't much to do wrong, when 
downloading the NSIS-based installer and just click "OK" everywhere.

And I found the "problem". Look at this:

P:\_virii>c:\clamav-devel\bin\clamscan p:\\_virii
p:\\_virii/Clean.dot.virus: WM.Buero.A FOUND
p:\\_virii/Happy99.exe.virus: Trojan.Happy99.SKA FOUND
p:\\_virii/Hotvir.arj.virus: OK
p:\\_virii/Hotvir.zip.virus: WM.Buero.A FOUND
p:\\_virii/Makro.arj.virus: OK
p:\\_virii/Nopde.doc.virus: WM.Nop.A FOUND
p:\\_virii/Nopde.zip.virus: OK
p:\\_virii/Normal.dot.virus: WM.Buero.A FOUND
p:\\_virii/Pack.zip.virus: Zip module failure
p:\\_virii/Pretty Park.exe.virus: W32.PrettyPark FOUND
p:\\_virii/profil CW.DOC.virus: W97M.Ethan FOUND
p:\\_virii/profil CW_mit Passwort.zip.virus: OK
p:\\_virii/Profilcw.doc.virus: W97M.Ethan FOUND

----------- SCAN SUMMARY -----------
Known viruses: 39349
Engine version: devel-20050725
Scanned directories: 1
Scanned files: 13
Infected files: 8
Data scanned: 0.12 MB
Time: 2.193 sec (0 m 2 s)

P:\_virii>c:\clamav-devel\bin\clamscan
/cygdrive/p/_virii/Clean.dot.virus: WM.Buero.A FOUND
/cygdrive/p/_virii/Happy99.exe.virus: OK
/cygdrive/p/_virii/Hotvir.arj.virus: OK
/cygdrive/p/_virii/Hotvir.zip.virus: WM.Buero.A FOUND
/cygdrive/p/_virii/Makro.arj.virus: OK
/cygdrive/p/_virii/Nopde.doc.virus: WM.Nop.A FOUND
/cygdrive/p/_virii/Nopde.zip.virus: OK
/cygdrive/p/_virii/Normal.dot.virus: WM.Buero.A FOUND
/cygdrive/p/_virii/Pack.zip.virus: Zip module failure
/cygdrive/p/_virii/Pretty Park.exe.virus: W32.PrettyPark FOUND
/cygdrive/p/_virii/profil CW.DOC.virus: W97M.Ethan FOUND
/cygdrive/p/_virii/profil CW_mit Passwort.zip.virus: OK
/cygdrive/p/_virii/Profilcw.doc.virus: W97M.Ethan FOUND

----------- SCAN SUMMARY -----------
Known viruses: 39349
Engine version: devel-20050725
Scanned directories: 1
Scanned files: 13
Infected files: 7
Data scanned: 0.12 MB
Time: 1.483 sec (0 m 1 s)

So there seems to be a problem and something is done different, when 
the file is passed to the scanner as cygwin path or as native windows 
path. Comparing the debug output it does find the virus directly 
after recognizing it as executable file. The other one starts priting 
informations about the file. Here is everything from the recognition 
point:

native:

LibClamAV debug: Recognized DOS/W32 executable/library/driver file
LibClamAV debug: Trojan.Happy99.SKA found in descriptor 4.
p:\\_virii\\happy99/Happy99.exe.virus: Trojan.Happy99.SKA FOUND

cygwin path:

LibClamAV debug: Recognized DOS/W32 executable/library/driver file
LibClamAV debug: Calculated MD5 checksum: 
78124c7632d29011c29894c55be4be58
LibClamAV debug: e_lfanew == 256
LibClamAV debug: Machine type: 80386
LibClamAV debug: NumberOfSections: 4
LibClamAV debug: TimeDateStamp: Wed Nov  3 15:07:27 1909
LibClamAV debug: SizeOfOptionalHeader: 224
LibClamAV debug: MajorLinkerVersion: 2
LibClamAV debug: MinorLinkerVersion: 25
LibClamAV debug: SizeOfCode: 2560
LibClamAV debug: SizeOfInitializedData: 5632
LibClamAV debug: SizeOfUninitializedData: 0
LibClamAV debug: AddressOfEntryPoint: 0x10000
LibClamAV debug: SectionAlignment: 65536
LibClamAV debug: FileAlignment: 512
LibClamAV debug: MajorSubsystemVersion: 3
LibClamAV debug: MinorSubsystemVersion: 10
LibClamAV debug: SizeOfImage: 327680
LibClamAV debug: SizeOfHeaders: 1024
LibClamAV debug: Subsystem: Win32 GUI
LibClamAV debug: NumberOfRvaAndSizes: 16
LibClamAV debug: ------------------------------------
LibClamAV debug: Section 0
LibClamAV debug: Section name: CODE
LibClamAV debug: VirtualSize: 4096
LibClamAV debug: VirtualAddress: 0x10000
LibClamAV debug: SizeOfRawData: 2560
LibClamAV debug: PointerToRawData: 0x600 (1536)
LibClamAV debug: Section contains executable code
LibClamAV debug: Section's memory is executable
LibClamAV debug: ------------------------------------
LibClamAV debug: Section 1
LibClamAV debug: Section name: DATA
LibClamAV debug: VirtualSize: 4096
LibClamAV debug: VirtualAddress: 0x20000
LibClamAV debug: SizeOfRawData: 4096
LibClamAV debug: PointerToRawData: 0x1000 (4096)
LibClamAV debug: Section's memory is writeable
LibClamAV debug: ------------------------------------
LibClamAV debug: Section 2
LibClamAV debug: Section name: .idata
LibClamAV debug: VirtualSize: 4096
LibClamAV debug: VirtualAddress: 0x30000
LibClamAV debug: SizeOfRawData: 1024
LibClamAV debug: PointerToRawData: 0x2000 (8192)
LibClamAV debug: Section's memory is writeable
LibClamAV debug: ------------------------------------
LibClamAV debug: Section 3
LibClamAV debug: Section name: .reloc
LibClamAV debug: VirtualSize: 4096
LibClamAV debug: VirtualAddress: 0x40000
LibClamAV debug: SizeOfRawData: 512
LibClamAV debug: PointerToRawData: 0x2400 (9216)
LibClamAV debug: ------------------------------------
LibClamAV debug: EntryPoint offset: 0x600 (1536)
/cygdrive/p/_virii/happy99/Happy99.exe.virus: OK

> I'm 95% sure that the answer to your problem is in the FAQ, so it's not 
> a problem of lack of documentation either.

It's not in the FAQ.
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