What you need to do is use official links for any precompiled windrop (never know what nasties other idiots may inject when they compile).
These links are official:
Windrop 1.6.18.exe or
windrop1.6.18-handlen32.exe
Your problem is directly related to this. You have used an infected (virus/trojan) build of windrop and are running anti-virus software most probably, and your installed windrop has been quarantined by your virus soft (this is why you can't find it). If your virus soft has a virus vault, checking it should reveal the infection plaguing that copy of windrop.
AVG virus soft's reaction to a suspicious copy of windrop I found on the web wrote:Oject name : Windrop.exe
Discovery : Trojan horse Agent MJV
Finder : System
File size : 2.34MB (2453887 bytes)
Healable : No
Source : Moved Object
Status : Infected (Quarantined)
Also, Windrop doesn't call itself windrop, it calls itself eggdrop. The windrop name is only given to the folder eggdrop is installed within on windows. If you want to use batch files I suggest something similar like below.
RunOnce.bat: eggdrop.exe -m eggdrop.conf
RunAfter.bat: eggdrop.exe
Pretty simple eh? There is also an easier way, simply open the run dialog (start>run) and type "DRIVE:\PATH\TO\EGGDROP.EXE" (keep the quotes if you have spaces in your path) then press ENTER (replacing of course 'drive' with your drive letter, and '\path\to\' with the path, this will restart any windrop instantly).