The first problem faced me while trying to upload is not being able to upload using Media manager at all.

to solve this problem I’ve added those two lines to .httaccess

SecFilterEngine Off
SecFilterScanPOST Off

Now the second problem was not being able to upload in front end, and to solve this problem did the following :

Go to admin panel -> Site Menu -> Global Configuration -> System -> Enable Flash Uploader (Set to no)

and thats it!