If its a problem developing with the printer and seems to be getting worse then that is potentially a sign that the USB controller on the printers mainboard might be going. One thing you could try would be to update the firmware on the printer. That may or may not help but its a possibility it will. Worst case is it will be the mainboard in the printer which will be expensive but if you are handy you can replace it yourself. Kent at Macmedia can also probably repair the board as well which would be a lot less expensive than replacing the board. That would also be less traumatic since the board will still have all of your machines configuration. If you replace the board you will want to use the firmware tools to back up its configuration and note the current firmware so you can load the same onto the replacement board. What version is the firmware on the printer? Also how long of a USB cable are you using? On trying a different USB cable did you go with the same brand cable? If its a fairly long one I might suggest trying a shorter one (even if it means moving the machine closer to test) just to rule out the length of the cable. Ours is on a 15 foot cable (Belkin brand cable) though and has no problem.
Back on the computer - try this on Production Manager. Under the top Edit menu, go to Preferences. Make sure "Print while ripping" is unchecked. If that is checked and the computer is ripping a file in multiple chunks then it might be busy ripping parts of the file while its also trying to print parts of it which can slow it down to the point that printing will pause while its starving for data to get to it fast enough. Depending on the processor in the computer you also might want to set the maximum number of RIP threads to be one less than what the computer has. Ours has a quad core Intel. I have it set to 3 on ours. I figure this maximizes the ability of the machine to RIP files while still leaving one processor core free for Windows to use for the operating system itself. If you have a dual core processor you might try setting it to 1. Do not count hyper threading cores as additional cores though. If you are unsure look at the computer properties and let me know what it says the processor is and I can tell you for sure. Attached shows where it says the specific processor (this is on my design workstation, way overkill for the rip). The first screen will also show how much ram you have and if you are running 32 or 64 bit Windows. If I look in Windows Device Manager mine shows 24 processors but realistically it is only 12 - the Xeon processors in this design workstation have hypertreading. Make sure on the main Production Manager window that the hard drive(s) shown at the bottom all have plenty of free space. The hard drive(s) settings for Production Manager are also in the preferences menu. If you have more than one drive I suggest having Flexi installed on C: as normal but setting the Archive, Jobs, and Temporary files pointed to a folder on another drive. Also the actual hard drive itself could be the culprit if it is a slow hard drive. If the hard drive is just too slow then it will not be able to move the data to the printer fast enough. If that is the case though then the printer would just pause while printing while it waits for more data but would start printing again on its own and you might have to look into upgrading the hard driver to a faster one. You also should occasionally clear out some of the old files in Production Manager (if you have them default to hold in the list). I delete old jobs out of ours about every two weeks or so keeping only the last 2 to 4 weeks of jobs in there. Also there is the "Clear Job Log" under the View menu in Production Manager which is also probably good to do once in a while but that log can also help in troubleshooting things. Also - what specific version of Flexisign?
Our prior computer for the RIP had 7200 rpm hard drives which worked fine and our current one has dual SSD's. We do use a dedicated computer for the RIP as well. It runs Windows 7 and Production Manager (we even have Windows set to automatically login and Production Manager is in the startup folder on the start menu so it is always running and ready). Nothing else is installed, it is not used for web surfing (it can just fine, we just don't use it for that unless its for downloading a new driver or update or something). You can install Flexi Pro on multiple machines, leave the dongle on the dedicated RIP computer. On the design computer we install the same Flexi (do not use Production Manager on the design computer(s)), when one of us opens Flexi if someone else already has it open on another computer you will get an error, if not it finds the dongle over the network on the RIP computer and opens right up. When you send a job it finds the Production Manager over the network and works great.
I guess getting ahead of myself on things to try though. If the printer simply stops responding totally, in other words the keypad will not respond and it will not do anything- display will be on and you might be able to get one or two key beeps then the keys will not respond or do anything at all then the printer has frozen up and will have to be powered off and back on. Ours does this once in a long while, maybe once in 2 months. However when it does do that I'm not sure if it is the printer itself or if possibly the computer sent a bad command of some sort that freaked it out. In the end it still could be one of many things. You might even have to try a different computer altogether to totally rule out the computer as the problem. If you have some other computer you could temporarily use (even if you had to borrow one) for this purpose I'd personally give that a try. As long as its reasonably capable then you could install Flexi on it and try running with it for a couple of days. Then you could just about 100% confirm that the problem is either the computer or the printer and then move onto the next logical steps. Obviously trying a different printer would not be quite as simple but if it still does it with a totally different computer then you at least can say with nearly 100% confidence that the printer is the issue.