Yesterday it happened it to me too. I had around 260MB remaining and I wanted to squeeze it out. So I started downloading 100MB files from link-removed.
10:20 PM: My usage was 1020 MB.
10:30 PM: I started the download of the first 100 MB file.
11:15 PM: The download got over.
11:16 PM: I tried to start the next download. But link-removed was asking me to wait for 203 minutes. So I disconnected and reconnected to get a new IP.
11:19 PM: Was reconnected and my balance was 1130MB.
11:20 PM: I started then next download.
11:55 PM: The second download also got over.
12:03 AM: I disconnected and reconnected.
My usage should ideally have been 1230MB or probably couple of MBs more. But here is what it shows in my usage history (see total... its showing only 1330 MB):
Click here to view my usage history
Dont know if it is really still a flaw in their system. But it worked for me last night