This may happen due to several things. You first need to check if the files from your pendrive aren't hidden. To do this, go to Start, open the Command Prompt by right clicking on it and choose Run as Administrator (the location may differ depending on your OS; it can usually be found on Start > Accessories > Command Prompt), and type
attrib *.* X: -r -s -h /s /d where X: represents the letter for your pendrive drive and hit Enter. After you did this, open the My Computer and explore the content of your pendrive. If it appears to be empty and the size of it is still 4 MB, try formatting it. You can do this by right click on it in My Computer > Format and press Start. This should fix your problem, but you will wipe all your data contained in the pendrive.