It seems that the present of the SEB is mostly due using FWHM instead of sigma when using single epoch spectra.
1) According to Peterson et al. (2004), Fig 3, when we use rms spectra then FWHM and sigma_{line} are equally valid and good enough to satisfy a virial relationship in the form where FWHM is linearly represents the virial velocity. Yet using single epoch spectrum is more like mean spectrum. Fig 4 of Peterson et al. (2004) shows that FWHM relationship, if it is considered as a virial relationship, might be represented in a nonlinear form of relationship between FWHM and virial velocity.
Fig 3 of Peterson et al. (2004)

Fig 4 of Peterson et al. (2004)

2) lets say we have the virial relation exist for both, mean and rms of the FWHM (by the way that's what Shen et al. (2008) work is based on) so we have:
$MBH_{mean} \propto \tau_{mean} \times FWHM_{mean}^{2}$\\
$MBH_{rms} \propto \tau_{rms} \times FWHM_{rms}^{2}$\\
However, from Fig 3 and Fig 4 (comparing the lower plots for FWHM using rms and mean) of Peterson et al. (2004) we approximately have (this is my key point):
$\tau_{rms} < \tau_{mean} for any given FWHM when FWHM > 3000 km/s$\\
$\tau_{rms} > \tau_{mean} for any given FWHM when FWHM < 3000 km/s$\\
(Indeed and by a little exaggeration, I can say that $\tau_{mean}$ is just a constant with some scatter! just cut out the two or three data points in far left of the plot 4-lower panel.)
2-2) Now, for a given FWHM (in which $FWHM_{mean}=FWHM_{rms}$) we have:
$\frac{MBH_{mean}}{\tau_{mean}} = \frac{MBH_{rms}}{\tau_{rms}}$\\
which can be re-written as:
$\frac{MBH_{mean}}{MBH_{rms}} = \frac{\tau_{mean}}{\tau_{rms}}$\\
Now, from (2-1) we had relations between $\tau_{mean}$ and $\tau_{rms}$ for two cases of FWHM above or bellow the 3000 km/s. lets apply them on (2-2) equation and we have:
$MBH_{mean} > MBH_{rms}$ for a given FWHM $>$ 3000 km/s\\
$MBH_{mean} < MBH_{rms}$ for a given FWHM $<$ 3000 km/s\\
which means, any calibration to virial relationship for FWHM will overestimates the BH masses for the highest mass (approximately when FWHM $>$ 3000 km/s) with respect to the true BH mass (based on rms spectra) and it underestimates the mass when FWHM is smaller than 3000 km/s.
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Here is the plot comparing Shen 2008 and R&H 2011 masses versus FWHM.
The pivot point here is about logFWHM=3.65 which is almost 4400 km/s (and not 3000 km/s).
