Thank you,
this is the solution.
I just replaced at4/20 by seq(0, max.yl, length.out=par("yaxp")[3]+1) so it
should work with any scale.
here is the final code that worked for me:

## R-Help 2014-05-28 asked by Bastian Pöschl solved by Gabor Grothendieck

library("zoo")

## generate some smooth timeseries
x1 <- c(38.2, 18.1, 83.2, 42.7, 22.8, 48.1, 81.8, 129.6, 52.0, 110.3)
x2 <- c(2.2, 0.8, 0.7, 1.6, 0.9, 0.9, 1.1, 2.8, 5.1, 2.1)

z1 <- zooreg(x1, start=as.POSIXct("2013-01-01 00:00:01"),
frequency=0.0000006)
z2 <- zooreg(x2, start=as.POSIXct("2013-01-01 00:00:20"),
frequency=0.0000006)
zt <- zooreg(rnorm(1050), start=as.POSIXct("2013-01-01 00:00:01"),
frequency=0.00007)

z<-merge(zt, z1, all = TRUE)
z<-merge(z, z2, all = TRUE)
Zf<-na.spline(z[,2:3], na.rm = FALSE)
##  ##  ##  ##

## function to round up to a number divisible by n (2011 by Owen Jones)
roundup <- function(x,n){ceiling(ceiling(x)/n)*n}
##  ##  ##  ##

## Plot How to match secondary Y-axis ticks to primary ones
plot(Zf$z1, ylim=c(0,signif(max(na.omit(Zf$z1)*1.05),2)), xlab="")
## use multiplication for even tick numbers and fake sekondary y-axis
max.yl<-roundup(max(na.omit(Zf$z2)), par("yaxp")[3])
multipl.yl<-max(na.omit(Zf$z2))/max.yl
multipl.z2<-signif(max(na.omit(Zf$z1)*1.05),2)/max.yl
lines(Zf$z2*multipl.z2, lty=2)
at4 <- axTicks(4)
axis(4, at = at4, seq(0, max.yl, length.out=par("yaxp")[3]+1))
abline(h = at4, lty = "dotted", col="grey")


The Result is a time series plot of two variables, with nice ticks at
primary and secondary y-axis at the same height connected with reference
lines and thus easy to read.


2014-05-28 12:56 GMT+02:00 Gabor Grothendieck <ggrothendieck@gmail.com>:

> On Wed, May 28, 2014 at 4:28 AM, Bastian Pöschl <bstan0578@gmail.com>
> wrote:
> > Thank you for the quick reply,
> >
> > your advice wasn't exactly what I was looking for.
> > The plot 1 of the example was ment to show my problem:
> > the secondary axis has it's first tick at the intersection with the
> x-axis
> > whereas the primary y-axis shows a nice little offset.
> >
> > Using your advice i copied the y axis and tried to solve the Problem "by
> > foot". Unfortunately the lable text isn't willing to center to the ticks
> >
> > Here is the code:
> >
> > ## R-Help 2014-05-28
> >
> > ## Test second. Y-Axix
> > library("zoo")
> >
> > ## generate some smooth timeseries
> > x1 <- c(38.2, 18.1, 83.2, 42.7, 22.8, 48.1, 81.8, 129.6, 52.0, 110.3)
> > x2 <- c(2.2, 0.8, 0.7, 1.6, 0.9, 0.9, 1.1, 2.8, 5.1, 2.1)
> >
> > z1 <- zooreg(x1, start=as.POSIXct("2013-01-01 00:00:01"),
> > frequency=0.0000006)
> > z2 <- zooreg(x2, start=as.POSIXct("2013-01-01 00:00:20"),
> > frequency=0.0000006)
> > zt <- zooreg(rnorm(1050), start=as.POSIXct("2013-01-01 00:00:01"),
> > frequency=0.00007)
> >
> > z<-merge(zt, z1, all = TRUE)
> > z<-merge(z, z2, all = TRUE)
> > Zf<-na.spline(z[,2:3], na.rm = FALSE)
> > ##  ##  ##  ##
> >
> > ## Plot How to match secondary Y-axis ticks to primary ones
> > plot(Zf$z1, ylim=c(0,signif(max(na.omit(Zf$z1)*1.05),2)), xlab="")
> >
> > ## function to round up to a number divisible by n (2011 by Owen Jones)
> > roundup <- function(x,n){ceiling(ceiling(x)/n)*n}
> > ##  ##  ##  ##
> >
> > ## use multiplication for even tick numbers and fake sekondary y-axis
> > max.yl<-roundup(max(na.omit(Zf$z2)), par("yaxp")[3])
> > multipl.yl<-max(na.omit(Zf$z2))/max.yl
> > multipl.z2<-signif(max(na.omit(Zf$z1)*1.05),2)/max.yl
> > lines(Zf$z2*multipl.z2, lty=2)
> > axis(4, labels = FALSE)
> > abline(h = axTicks(4), lty = "dotted", col="grey")
> > lablist.y<-seq(0, max.yl, length.out=par("yaxp")[3]+1)
> >
> > ## my problem!! text doesn't center to the ticks
> > text(y = seq(0, signif(max(na.omit(Zf$z1)*1.05),2),
> > length.out=par("yaxp")[3]+1),
> > par("usr")[2]+(par("usr")[2]-par("usr")[1])*0.025, labels = lablist.y,
> srt =
> > 90, pos = 4, xpd = TRUE)
> >
>
> If the problem is to center the labels on the right y axis then try this:
>
> plot(Zf$z1, ylim=c(0,signif(max(na.omit(Zf$z1)*1.05),2)), xlab="")
> lines(Zf$z2*multipl.z2, lty=2)
>
> at4 <- axTicks(4)
> axis(4, at = at4, at4/20)
> abline(h = at4, lty = "dotted", col="grey")
>

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