I keep reading about a config file for cgminer but I can't find it. Is it made when you make changes to cgminer with commands wail it is running? I start cgminer with a bat file. This works fine but I am trying to learn more about cgminer. Am i doing something wrong? I also can't figure out what they mean when they say compiling cgminer. 
You can configure cgminer by config file or by command line arguments (in a bat file) or both at the same time. Either one is fine. Ignore everything about compiling CG miner, it wont apply to you.
If you have cgminer running, you can use the keyboard to navigate to settings and write the config file, but this isn't really needed if you use a batch (and might be confusing!)
I can't stress enough that the hashrate your pool is reporting will only be +/- correct after a couple hours. If you use the eligius pool, you can see your 12 hour, 3 hour etc hashrate. When I test perf I look at the 3hour rate.
If you see your hash rate go down slowly, it's probably just bad luck, you getting hard work, pool thinks you are a bit slower than you would be with "average difficulty" work.
Example: My BFGMiner reports 376ghps (which is dead on) but my 12 hour average on eligius is between 370 and 380 and my 3 hour average can range from 350 to 420.
If you want me too look at it, do this:
-at the end of your command line in your .bat file, add " -D 2>log.txt", then save the .bat. (the -D will tell cgminer to give you more information (debug) and the 2>log.txt will save the output to a text file)
-Stop cgminer.
-Run the bat. Let cgminer run for a couple minutes. Don't get scared by all the crazy lines flashing by.
-Stop CG miner.
-Remove the "-D 2>log.txt" from your bat.
-Run bat again to mine normally.
-Then send me the log file (log.txt) that should be in your cg miner directory. (Hint: you can upload the text file on pastebin.com, and copy the link here, so everybody can look at it)
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I tried fgminer. I ran fine but it could not find the baby jet.
What am i doing wrong. I used a bat file to start it and the simple commands to start the program looked close to cgminer.
What am i doing wrong. I used a bat file to start it and the simple commands to start the program looked close to cgminer.
You will need the driver for BFGminer I have posted a couple pages back:
https://www.dropbox.com/s/w607kpr4j2fh0o0/Windows-Mining-Infs.zip
-Unzip
-Go to windows device manager
-Right click the babyjet (M1 device) under USB devices
-Click update driver software
-"Browse..."
-"Let me pick....."
-"Have disk"
-Chose your extracted babyjet folder.
Once the driver updated, you should see the new "Babyjet" device under Com Ports in device manager, BFGMiner 3.10 will use it without further configuration, except pool, worker etc.
Remember that if you install this driver, CGMiner wont work anymore, if you want to use CGMiner again, you will have to run Zadig again, point to Babyjet, WinUSB, install.