Are you talking about trying to enter live or correspondence tournaments? Live chess doesn't track timeouts as a percentage, for the reasons you gave. Correspondence tournaments have their own separate timeout stat, and that's what's hurting you because yours is 50% right now. However, most of your games are fairly old, so it shouldn't be long before your timeouts drop out of the most recent 90-day window. As long as you don't add any more timeouts, you'll quickly be back to a low value or even 0%.
EDIT: In case you're not aware, it's only the past 90 days that is monitored when determining the timeout ratio.
I have recently tried to enter some tournaments but have been rejected because my time-out rate is more than 10%. I have recently played quite a number of blitz live games (10 minute games) and obviously lost quite a number of them on time. Could this be the reason? If so one should refrain from playing blitz games because a large precentage of them are won and lost on time. Apart from the live games I think that I have lost only one or two out of a total of 249 standard and chess 960 games on time. My stats show a timeout ratio of 50%.
Can someone shed some light on the situation?