(Click here for an in depth discussion of Yovel in the online book "Yovel & Geulah".)
According to the Rambam, Yovel is counted as follows:
There are 7 Shmitah cycles, followed by a Yovel year. The year after Yovel is year 1 of the next Shmitah cycle. This is the opinion of the Chachamim brought in the Gemara. Yovel occurs every 50 years.
However, that is not the only opinion. Rebbi Yehudah says that we count this way:
There are 7 Shmitah cycles, followed by a Yovel year. Yovel counts as the 50th year of the prior cycle, and the 1st year of the next cycle. The year after Yovel is the 2nd year of the Shmitah cycle. Yovel occurs every 49 years.
Perhaps it is not that the Geonim held that we don't count Yovel when the Beit HaMikdash isn't standing, but that the halachah is to use the counting system of Rebbi Yehudah in times of Galus, when Shmitah is on a sort of autopilot, which on the outside (for halachah) seems as if we count Shmitah alone.
So while the 2nd Beit HaMikdash stood, Yovel years were:
3415 + 50n where 1 <= n <= 9 (3415 was the year before the counting of Yovel began in the time of the 2nd Beit HaMikdash)
However, when the 2nd Beit HaMikdash was destroyed, Yovel switched to:
3816 + 49n where 1 <= n <= 44 (3816 was the year after the last Yovel counted of the 2nd Beit HaMikdash)
By this, we find that the last Yovel year was 5727 (1967CE), the year of the 6-Day War. This was the 48th Yovel year starting from the time of Ezra in 3416. The Yovel year which is 49 years later is 5776. Perhaps the year following would be a fitting time for the Sanhedrin to assume/resume its role in counting of Shmitah and Yovel, to assume its role of leadership of Am Yisrael. This next Yovel would start the 49th Yovel period. Rather fitting that the Sanhedrin would count the last Yovel before the 50th Yovel, a Yovel of Yovels.
It is nearly time to take Am Yisrael off of autopilot.