Just to clarify that "remove custom font" means changing the value for font-family in the settings for hterm, from this:
   "Inconsolata","Everson Mono", FreeMono, "Menlo", "Terminal", monospace
to this (which is/was the default value): 
   "Everson Mono", FreeMono, "Menlo", "Terminal", monospace

repros for me, Linux Version 54.0.2840.59 (64-bit)
Also w/ Inconsolata

A Math.round(rulerSize.height / numberOfLines) appears to help this issue.

But Inconsolate rendering is still deteriorated (gap lines visible between rows of solids, e.g. cacademo).

No problems afaict on hterm 1.58, thus[ hterm.ScrollPort.prototype.measureCharacterSize is prime suspect.

afakhry@ - Could you please provide any update on this issue.

Thanks...!!

Can you provide exact steps to repro? I haven't seen this issue repro for me at all since  bug 633924  was fixed.

Exact steps to reproduce on Windows 7:
1) Install chrome browser
2) Install app 'Secure Shell' from the chrome web store
   Version: 0.8.34.4
   Updated: September 19, 2016
3) Windows Control Panel > Fonts > install font 'Inconsolata' (url in orig post)
4) Secure Shell > options > font-family > Prepend existing value with '"Inconsolata", '
5) Start secure shell and connect to a host
6) At the command line prompt, hit lots of 'enter' to get to the bottom of the viewing pane
7) Start entering dummy commands Eg '1', '2', '3', etc.  
7) Within about 10-20 comands, the prompt dissappears below viewing pane. See attached screenshot faulty-B.png
8) Within another 10-20 dummy commands, the prompt line reappears at bottom of viewing pane where it belongs.  See attached screenshot notFaulty-B.png

HTH
-Stew

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Sorry I should mentioned the versions of Chrome where it is reproducible on Win7
  Version 53.0.2785.143 m
  Version 54.0.2840.59 m
-Stew

Able to repro as described in comment #6 on Secure Shell version 0.8.34.4. I'll work on a fix.

Here's my analysis. I believe the issue is the use of lib.f.smartFloorDivide() to calculate the topRowIndex. smartFloorDivide() favors flooring unless the difference is very small (< 0.0001)! This results in the case of the "Inconsolata" font to have the visible area shifted one row above.

Using Math.round() in:

topRowIndex = Math.round(this.screen_.scrollTop / this.characterSize.height);

fixes the issue for the "Inconsolata" font and still works with the default font.

+wilford@ who introduced lib.f.smartFloorDivide().

reference CL:
https://chromium.googlesource.com/apps/libapps/+/f4e90e86bec06b124eaf4a0c01ea924cdc7f49a4%5E%21/

Since have the same problem.
Here is my setting,a default setting without any change.
Font Family :DejaVu Sans Mono", "Everson Mono", FreeMono, "Menlo", "Terminal", monospace
Font-size :16
Font-soomthing :antialiased

Did this Font like Inconsolata also cause problem?

I found that almost always favoring to floor the topRowIndex is the root cause of the issue. It leads to the problem showing for some fonts and renderer zooms.

I'll upload a fix.

The following revision refers to this bug:
  https://chromium.googlesource.com/apps/libapps/+/6cec52ab8e442a4ec35c16907187f4e1a21a286f

commit 6cec52ab8e442a4ec35c16907187f4e1a21a286f
Author: Ahmed Fakhry <afakhry@google.com>
Date: Fri Oct 28 18:01:46 2016

Fix Hterm's last line sometimes disappearing for some fonts and zooms

We used to almost always prefer to floor the value of the topRowIndex
using lib.f.smartFloorDivide(). This round error didn't work in all cases
for some fonts and some zooms ('Ctrl' + '+'/'-'). It led to the index of
the top visible row being one-too-few, hence hiding the last row.

BUG= chromium:648845 
TEST=mkdeps.sh, mkzip.sh --nopromote, load it on Linux Chrome, add
the font to "Inconsolata" (must be installed first) from the options
page, type 'seq 10000' several times, try differnt zooms and sizes.
The last row must never be hidden.

Change-Id: I557ecbb6029ec1c55b067b2bce04d9378349c661
Reviewed-on: https://chromium-review.googlesource.com/404990
Reviewed-by: Rob Ginda <rginda@chromium.org>
Tested-by: Rob Ginda <rginda@chromium.org>

[modify] https://crrev.com/6cec52ab8e442a4ec35c16907187f4e1a21a286f/hterm/js/hterm_scrollport.js