EDIT after resolving: offtopic since the issue was that the php extension for ImageMagick was not installed on the server - therefore not Craft-related.
Because .gif's were not being transformed properly (only the first frame) I figured ImageMagick was not doing the image transforms.
Therefore I updated the general config file with the line to set the imageDriver to ImageMagick ('imageDriver' => 'imagick'). However, as from that point whenever I tried to upload an asset in the control panel, the black loading bar appeared, instantly full, and the loading icon in the top right kept spinning. The loading bar did not disappear, nor did the file get uploaded.
As soon as I removed this line from the general config, the uploading worked as normal again.
I have tested my server and ImageMagick is installed (v6.8.3-6). I am running PHP 5.4.
I am not running any plugins. The only other setting I have in the general config file is 'generateTransformsBeforePageLoad' => true
Does anybody know what could cause this issue? I would like to use ImageMagick for all the transfers, but of course especially for the .gif's.