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This is not a very strange bug, like every bug, it causes your code stop working properly. A strange bug would be creating you a multitasking environment while you are trying to write a boot loader, this is ABSOLUTELY NOT a very strange bug. Thats all I can say...
since you do not check sectors were loaded correctly (CF flag) after you called INT 13, i'm not surprised you get Very Strange Things (tm) occuring ... You should know that the Floppy Controller may fail one or two time reading a sector before it succeeds ... It may not be calibrated very well, etc. So you have to try up to three times before you actually can tell it's not working (yeah, i know: it suxx, but that's the way it is), and you should certainly not assume it will succeed without checking the error code.