I got a similar issue even with DT 0.4, I am afraid. The example app runs fine, but in my own dashboard (much more complex), regular tables work fine, but DT tables don't. I cannot think of a way to reproduce this, though.
Here is the session info (I've updated DT to 0.5.1. in the meanwhile, but to no avail):
> sessionInfo() R version 3.5.1 (2018-07-02) Platform: x86_64-pc-linux-gnu (64-bit) Running under: Debian GNU/Linux 9 (stretch) Matrix products: default BLAS: /usr/lib/openblas-base/libblas.so.3 LAPACK: /usr/lib/libopenblasp-r0.2.19.so locale:  LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C  LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8  LC_MONETARY=en_US.UTF-8 LC_MESSAGES=C  LC_PAPER=en_US.UTF-8 LC_NAME=C  LC_ADDRESS=C LC_TELEPHONE=C  LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C attached base packages:  stats graphics grDevices utils datasets methods base other attached packages:  bindrcpp_0.2.2 plotly_4.8.0 Hmisc_4.1-1  Formula_1.2-3 survival_2.42-6 lattice_0.20-35  rlang_0.3.0.1 gower_0.1.2 echarts4r_0.1.2.9000  dygraphs_220.127.116.11 mondate_0.10.01.02 shinyBS_0.61  shinydashboardPlus_0.5.0 htmltools_0.3.6 timevis_0.4  shinydashboard_0.7.0 shinyWidgets_0.4.3 shinythemes_1.1.1  flexdashboard_0.5.1.1 lubridate_1.7.4 data.table_1.11.4  DT_0.5.1 forcats_0.3.0 stringr_1.3.1  dplyr_0.7.6 purrr_0.2.5 readr_1.1.1  tidyr_0.8.2 tibble_1.4.2 ggplot2_3.0.0  tidyverse_1.2.1 shiny_1.1.0
After digging around some more, we've managed to locate an error. It is still a strange one, however.
The setup is as follows: we have a filter that impacts data generation for two DT tables. Both tables have separate
DTOutput() couplings. In principle, they should be independent from each other, as the only common ancestor that they have is the global data frame, plus, of course, the filter itself. Now, the filter works fine as long as the number of rows in each table is greater than 0. However, if even one of the tables has zero rows, BOTH tables are not updated (or not rendered, when this is upon initialization).