The new MT4 Build 600 keeps the indicators and EA files in a different location. So you’ll need to copy and paste them from your current mt4 to the new place. This article by DailyFx.com explains very nicely how to remedy this problem. Thanks Jason Rogers.
Where can I find my EAs, indicators, etc. on MT4 Build 600?
The latest version of FXCM MetaTrader 4 now saves your expert advisors, indicators, profiles, etc. in a different location on your computer. If you do not see your EAs and indicators in the navigator folder, your MT4 files are most likely still saved in the old folder location and are not recognized by the new version build of MT4.
Please follow the instructions below to move your files to the correct directory on build 600 of MT4.
1. First, find where you have your MT4 files saved currently. Below are the file types and location where these files may be currently saved on your computer. You may also want to check your desktop or downloads folders to see if you have copies of these files saved there.
2. Open MT4 > click on File > Open data folder > then double click the MQL4 folder. This will show you where your experts, indicators, etc. should be saved on your computer. Unless you have UAC settings disabled the folder location will be C:Users[user name]AppDataRoamingMetaQuotesTerminal[32 character long MT4 ID]MQL4
3. Copy the files from the old location to the new location. For your EA’s, for example, you will copy the contents of the C:Program Files (x86)FXCM MetaTrader 4experts folder to C:Users[user name]AppDataRoamingMetaQuotesTerminal[32 character long MT4 ID]MQL4Experts
How to Recompile EAs and Indicators on MT4 Build 600
MetaEditor has changed in MT4 build 600 and as a result some expert advisors and indicators may have to be recompiled. Please follow the steps below to recompile your experts and indicators.
1. Open MT4 > go to File > Open data folder > double click on the MQL4 folder
2. Double click on the name of the expert advisor or indicator to open the file in MetaEditor.
3. If there are any errors when compiling the expert or indicator you will see those appear at the bottom of MetaEditor. You will need to address these errors before you are able to add the expert or indicator onto an MT4 chart.
Backing up files on MT4 Build 600
Please follow the instructions below to save backups for your MT4 files (expert advisors, indicators, libraries, templates, and profiles). It’s often a good idea to save a backup before uninstalling/reinstalling MT4, transferring files to another installation of MT4, etc.
1. Create a new folder where you would like for your backup files to be saved. To create a new folder right click > go to New > click on Folder.
2. Navigate to where your where your MT4 files are saved on your computer. Depending on the build of MT4 you are using they could be saved in a couple of different locations.
a. Build 509 and older: C:Program Files (x86)FXCM MetaTrader 4expertsb. Build 600: Open MT4 > go to File > Open data folder > then double click on the MQL4 folder. Depending on your settings this may go to either folder location below.
i. C:Users[user name]AppDataRoamingMetaQuotesTerminal[32 character long MT4 ID]MQL4Expertsii. C:Program Files (x86)FXCM MetaTrader 4MQL4
3. Copy the folders you would like to save and paste them into the new MT4 backup folder.
Insufficient Permission to Uninstall MT4
If you receive an error message when you are trying to uninstall MT4 stating you do not have sufficient privileges you will need to edit a value in your computer’s registry.
1. Press Start then type in “regedit” and press enter. This will bring up your computer’s registry.
2. Press ctrl + F and type in “EnableLUA”. (You can also find this by going through the menu tree on the left. You would need to go to HKEY_LOCAL_MACHINE > Software > Microsoft > Windows > CurrentVersion > Policies > System)
3. Double click on EnableLUA in the right side of the registry editor window.
4. Change the value data from 1 to 0 and press OK.
5. Close the registry editor window and restart your computer. After you have restarted your computer, you will be able to uninstall MT4 though the task manager.
6. Repeat Steps 1 to 4 above only this time change the value data back from 0 to 1 and press OK.
7. Close the registry editor window and restart your computer. After you have restarted your computer, UAC will be enabled on your computer as it was previously.
Source: http://www.dailyfx.com/forex_forum/fxcm-mt4/627008-mt4-build-600-problems.html#post1850261